{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Protein-ligand Docking tutorial using BioExcel Building Blocks (biobb)\n",
    "### -- *PDB Cluster90 Binding Site Version* --\n",
    "\n",
    "***\n",
    "This tutorial aims to illustrate the process of **protein-ligand docking**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Mitogen-activated protein kinase 14** (p38-α) protein (PDB code [3HEC](https://www.rcsb.org/structure/3HEC)), a well-known **Protein Kinase enzyme**, \n",
    " in complex with the FDA-approved **Imatinib**, (PDB Ligand code [STI](https://www.rcsb.org/ligand/STI), DrugBank Ligand Code [DB00619](https://go.drugbank.com/drugs/DB00619)), a small molecule **kinase inhibitor** used to treat certain types of **cancer**. \n",
    " \n",
    "The tutorial will guide you through the process of identifying the **active site cavity** (pocket) without previous knowledge, and the final prediction of the **protein-ligand complex**. \n",
    "\n",
    "Please note that **docking algorithms**, and in particular, **AutoDock Vina** program used in this tutorial, are **non-deterministic**. That means that results obtained when running the workflow **could be diferent** from the ones we obtained during the writing of this tutorial (see [AutoDock Vina manual](http://vina.scripps.edu/manual.html)). We invite you to try the docking process several times to verify this behaviour. \n",
    "***\n",
    "\n",
    "<div style=\"background:#b5e0dd; padding: 15px;\"><strong>Important:</strong> it is recommended to execute this tutorial step by step (not as a single workflow execution, <strong><em>Run All</em></strong> mode), as it has interactive selections.</div>\n",
    "\n",
    "## Settings\n",
    "\n",
    "### Biobb modules used\n",
    "\n",
    " - [biobb_io](https://github.com/bioexcel/biobb_io): Tools to fetch biomolecular data from public databases.\n",
    " - [biobb_structure_utils](https://github.com/bioexcel/biobb_structure_utils): Tools to modify or extract information from a PDB structure file.\n",
    " - [biobb_chemistry](https://github.com/bioexcel/biobb_chemistry): Tools to perform chemoinformatics processes.\n",
    " - [biobb_vs](https://github.com/bioexcel/biobb_vs): Tools to perform virtual screening studies.\n",
    " \n",
    "### Auxiliar libraries used\n",
    "\n",
    " - [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.\n",
    " - [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
    " - [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.\n",
    "\n",
    "### Conda Installation and Launch\n",
    "\n",
    "```console\n",
    "git clone https://github.com/bioexcel/biobb_wf_virtual-screening.git\n",
    "cd biobb_wf_virtual-screening\n",
    "conda env create -f conda_env/environment.yml\n",
    "conda activate biobb_VS_tutorial\n",
    "jupyter-nbextension enable --py --user widgetsnbextension\n",
    "jupyter-nbextension enable --py --user nglview\n",
    "jupyter-notebook biobb_wf_virtual-screening/notebooks/clusterBindingSite/wf_vs_clusterBindingSite.ipynb\n",
    "  ``` \n",
    "\n",
    "***\n",
    "## Pipeline steps\n",
    " 1. [Input Parameters](#input)\n",
    " 2. [Fetching PDB Structure](#fetch)\n",
    " 3. [Extract Protein Structure](#extractProtein)\n",
    " 4. [Computing Protein Cavities (fpocket)](#fpocket)\n",
    " 5. [Filtering Protein Cavities (fpocket output)](#fpocketFilter)\n",
    " 6. [Extract Pocket Cavity ](#fpocketSelect)\n",
    " 7. [Generating Cavity Box ](#cavityBox)\n",
    " 8. [Downloading Small Molecule](#downloadSmallMolecule)\n",
    " 9. [Converting Small Molecule](#sdf2pdb)\n",
    " 10. [Preparing Small Molecule (ligand) for Docking](#ligand_pdb2pdbqt)\n",
    " 11. [Preparing Target Protein for Docking](#protein_pdb2pdbqt)\n",
    " 12. [Running the Docking](#docking)\n",
    " 13. [Extract a Docking Pose](#extractPose)\n",
    " 14. [Converting Ligand Pose to PDB format](#pdbqt2pdb)\n",
    " 15. [Superposing Ligand Pose to the Target Protein Structure](#catPdb)\n",
    " 16. [Comparing final result with experimental structure](#viewFinal)\n",
    " 17. [Questions & Comments](#questions)\n",
    " \n",
    "***\n",
    "<img src=\"https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png\" alt=\"Bioexcel2 logo\"\n",
    "\ttitle=\"Bioexcel2 logo\" width=\"400\" />\n",
    "***\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"input\"></a>\n",
    "## Input parameters\n",
    "**Input parameters** needed:\n",
    "\n",
    " - **pdb_code**: PDB code of the experimental complex structure (if exists).<br>\n",
    "In this particular example, the **p38α** structure in complex with the **Imatinib drug** was experimentally solved and deposited in the **PDB database** under the **3HEC** PDB code. The protein structure from this PDB file will be used as a **target protein** for the **docking process**, after stripping the **small molecule**. An **APO structure**, or any other structure from the **p38α** [cluster 100](https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22sequence%22%2C%22parameters%22%3A%7B%22target%22%3A%22pdb_protein_sequence%22%2C%22value%22%3A%22RPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPP%22%2C%22identity_cutoff%22%3A1%2C%22evalue_cutoff%22%3A0.1%7D%2C%22node_id%22%3A0%7D%2C%22return_type%22%3A%22polymer_entity%22%2C%22request_options%22%3A%7B%22pager%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22scoring_strategy%22%3A%22combined%22%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%7D%2C%22request_info%22%3A%7B%22src%22%3A%22ui%22%2C%22query_id%22%3A%22bea5861f8b38a9e25a3e626b39d6bcbf%22%7D%7D) (sharing a 100% of sequence similarity with the **p38α** structure) could also be used as a **target protein**. This structure of the **protein-ligand complex** will be also used in the last step of the tutorial to check **how close** the resulting **docking pose** is from the known **experimental structure**. \n",
    " -----\n",
    " - **ligandCode**: Ligand PDB code (3-letter code) for the small molecule (e.g. STI).<br>\n",
    "In this particular example, the small molecule chosen for the tutorial is the FDA-approved drug **Imatinib** (PDB Code STI), a type of cancer growth blocker, used in [diferent types of leukemia](https://go.drugbank.com/drugs/DB00619)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b3595cf9423641d193d48fa2390912d6",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": []
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import nglview\n",
    "import ipywidgets\n",
    "\n",
    "pdb_code = \"3HEC\"         # P38 + Imatinib\n",
    "\n",
    "ligand_code = \"STI\"       # Imatinib"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"fetch\"></a>\n",
    "***\n",
    "## Fetching PDB structure\n",
    "Downloading **PDB structure** with the **protein molecule** from the PDBe database.<br>\n",
    "Alternatively, a **PDB file** can be used as starting structure. <br>\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [Pdb](https://biobb-io.readthedocs.io/en/latest/api.html#module-api.pdb) from **biobb_io.api.pdb**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:15:49,040 [MainThread  ] [INFO ]  Downloading: 3hec from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hec.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:15:49,530 [MainThread  ] [INFO ]  Writting pdb to: download.pdb\n",
      "2021-05-17 15:15:49,534 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_io.api.pdb import pdb\n",
    "\n",
    "download_pdb = \"download.pdb\"\n",
    "prop = {\n",
    "  \"pdb_code\": pdb_code,\n",
    "  \"filter\": [\"ATOM\", \"HETATM\"]\n",
    "}\n",
    "\n",
    "pdb(output_pdb_path=download_pdb,\n",
    "    properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"vis3D\"></a>\n",
    "### Visualizing 3D structure\n",
    "Visualizing the downloaded/given **PDB structure** using **NGL**.<br><br>\n",
    "Note (and try to identify) the **Imatinib small molecule (STI)** and the **detergent (β-octyl glucoside) (BOG)** used in the experimental reservoir solution to obtain the crystal."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "346ac8bda3fd4ab5acffec4e58bc7c69",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view = nglview.show_structure_file(download_pdb, default=True)\n",
    "view.center()\n",
    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
    "\n",
    "view.render_image()\n",
    "view.download_image(filename='ngl1.png')\n",
    "view"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src='ngl1.png'></img>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"extractProtein\"></a>\n",
    "***\n",
    "## Extract Protein Structure\n",
    "Extract **protein structure** from the **downloaded PDB file**. Removing **any extra molecule** (ligands, ions, water molecules). <br><br>\n",
    "The **protein structure** will be used as a **target** in the **protein-ligand docking process**. \n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [extract_molecule](https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.extract_molecule) from **biobb_structure_utils.utils.extract_molecule**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:15:55,068 [MainThread  ] [INFO ]  Creating ed60c66d-be1b-48cd-9551-5411add09a64 temporary folder\n",
      "2021-05-17 15:15:55,876 [MainThread  ] [INFO ]  check_structure -i /home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/download.pdb -o pdb_protein.pdb --force_save --non_interactive command_list --list ed60c66d-be1b-48cd-9551-5411add09a64/extract_prot.lst\n",
      "\n",
      "2021-05-17 15:15:55,879 [MainThread  ] [INFO ]  Exit code 0\n",
      "\n",
      "2021-05-17 15:15:55,884 [MainThread  ] [INFO ]  ===============================================================================\n",
      "=                   BioBB structure checking utility v3.7.2                   =\n",
      "=                 A. Hospital, P. Andrio, J.L. Gelpi 2018-20                  =\n",
      "===============================================================================\n",
      "\n",
      "Warning: sequence features only available in mmCIF format or with external fasta input\n",
      "Structure /home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/download.pdb loaded\n",
      " Title: \n",
      " Experimental method: unknown\n",
      " Resolution: None A\n",
      "\n",
      " Num. models: 1\n",
      " Num. chains: 1 (A: Protein)\n",
      " Num. residues:  420\n",
      " Num. residues with ins. codes:  0\n",
      " Num. HETATM residues:  91\n",
      " Num. ligands or modified residues:  2\n",
      " Num. water mol.:  89\n",
      " Num. atoms:  2814\n",
      "Small mol ligands found\n",
      "STI A1\n",
      "BOG A353\n",
      "\n",
      "\n",
      "Step 1: ligands --remove All\n",
      "\n",
      "Running ligands. Options: --remove All\n",
      "2 Ligands detected\n",
      " STI A1\n",
      " BOG A353\n",
      "Ligands removed All (2)\n",
      "\n",
      "Step 2: water --remove Yes\n",
      "\n",
      "Running water. Options: --remove Yes\n",
      "89 Water molecules detected\n",
      "89 Water molecules removed\n",
      "Command list completed\n",
      "Final Num. models: 1\n",
      "Final Num. chains: 1 (A: Protein)\n",
      "Final Num. residues:  329\n",
      "Final Num. residues with ins. codes:  0\n",
      "Final Num. HETATM residues:  0\n",
      "Final Num. ligands or modified residues:  0\n",
      "Final Num. water mol.:  0\n",
      "Final Num. atoms:  2668\n",
      "Structure saved on pdb_protein.pdb\n",
      "\n",
      "2021-05-17 15:15:55,887 [MainThread  ] [INFO ]  Removing ed60c66d-be1b-48cd-9551-5411add09a64 temporary folder\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_structure_utils.utils.extract_molecule import extract_molecule\n",
    "\n",
    "pdb_protein = \"pdb_protein.pdb\"\n",
    "\n",
    "extract_molecule(input_structure_path=download_pdb,\n",
    "             output_molecule_path = pdb_protein)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"vis3D\"></a>\n",
    "### Visualizing 3D structure\n",
    "Visualizing the downloaded/given **PDB structure** using **NGL**.<br><br>\n",
    "Note that the **small molecules** included in the original structure are now gone. The new structure only contains the **protein molecule**, which will be used as a **target** for the **protein-ligand docking**. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "25d4f0e0914b4493b0c635cd01cf39e4",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view = nglview.show_structure_file(pdb_protein, default=True)\n",
    "view.center()\n",
    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
    "\n",
    "view.render_image()\n",
    "view.download_image(filename='ngl2.png')\n",
    "view"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src='ngl2.png'></img>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"bindingSite\"></a>\n",
    "***\n",
    "## Computing Protein Cavities (Cluster90 Binding Site)\n",
    "Computing the **protein cavities** (pockets) using information from the **PDB Cluster90**. The **PDB Cluster90** is a collection derived from the **PDB database**, containing structures having **less than 90% sequence identity** to each other. The **Cluster90 Binding Site** is using information from all the structures of the **Cluster90 collection** for a particular **input protein** to discover the possible **binding sites** from **small molecules** attached to **similar proteins**. <br>\n",
    "\n",
    "These **cavities** will be then used in the **docking procedure** to try to find the **best region of the protein surface** where the small molecule can **bind**. <br><br>\n",
    "Although in this particular example we already know the **binding site** region, as we started from a **protein-ligand complex** structure where the ligand was located in the same **binding site** as **Imatinib** is binding, this is not always the case. In the cases where we do not know these regions, the **Cluster90 binding site** utility will help us identifying the possible **binding sites** of our **target protein**.<br>\n",
    "<br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [pdb_cluster_zip](https://biobb-io.readthedocs.io/en/latest/api.html#module-api.pdb_cluster_zip) from **biobb_io.api.pdb_cluster_zip**\n",
    " - [bindingsite](https://biobb-vs.readthedocs.io/en/latest/utils.html#module-utils.bindingsite) from **biobb_vs.utils.bindingsite**\n",
    "***"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"cluster90\"></a>\n",
    "### Getting Cluster 90 collection \n",
    "Extracting the **Cluster90** collection from the input **PDB structure**. The collection will contain all the structures in the **PDB database** having **less than 90% sequence identity** to the input structure (our target protein).<br><br>\n",
    "*Please note that depending on the size of the cluster, the execution can take a while (minutes).*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:03,254 [MainThread  ] [INFO ]  Cluster: 90 of pdb_code: 3hec\n",
      " List: {'1wbo', '5n67', '5o8v', '4fa2', '1ouy', '3nnv', '4r3c', '1wbv', '3o8u', '4loq', '5n63', '3fln', '5o90', '1kv2', '3lfb', '4f9w', '4aa0', '3rin', '3new', '3zs5', '2oza', '1ouk', '3mh1', '3o8p', '1ywr', '3obg', '3p7c', '3bv3', '5etc', '3p78', '1wbw', '3od6', '2zb0', '4f9y', '1lew', '5tco', '3p5k', '2rg5', '2yis', '1bmk', '2npq', '3iw5', '2baq', '3hp2', '1wfc', '3oc1', '4eh4', '3kf7', '2bal', '5xyy', '3flq', '1w82', '3nww', '3kq7', '3ha8', '4tyh', '1m7q', '3itz', '3zsi', '3fls', '3s3i', '3lfc', '3mpt', '4dlj', '3lhj', '3fmn', '5mz3', '1oz1', '4a9y', '5lar', '4eh3', '1r39', '3mw1', '3k3i', '3dt1', '2onl', '1bl7', '3fmj', '3hec', '3hv6', '4kip', '4loo', '3fkn', '3iw8', '1a9u', '3fc1', '3mvm', '3uvq', '4eh9', '3ds6', '1di9', '3tg1', '3zya', '4l8m', '4dli', '2lgc', '3flw', '1w84', '3c5u', '3ctq', '3fly', '3fml', '3u8w', '2fst', '5mtx', '5n66', '2fso', '2gfs', '5eti', '3mpa', '3heg', '3nnu', '2y8o', '2qd9', '3zsg', '5n68', '1r3c', '2puu', '5etf', '3p4k', '3lfd', '5ml5', '5n65', '2yix', '1w83', '3uvr', '4eh7', '4kin', '3fmm', '3mh3', '3nnx', '5n64', '3gfe', '5omg', '2baj', '3fmk', '2zb1', '3hvc', '1kv1', '3d83', '3fi4', '3fkl', '3gi3', '4eh6', '3fl4', '3lff', '3k3j', '3huc', '3obj', '3uvp', '3pg3', '1ian', '3bv2', '4aac', '1wbn', '3lfe', '1wbs', '1ove', '3mh2', '4eh8', '2fsl', '5o8u', '2ewa', '1lez', '4e5a', '3bx5', '3ocg', '4geo', '2rg6', '3gcp', '3oef', '3hub', '4ewq', '1bl6', '4e6a', '4aa4', '2gtn', '4e5b', '4ka3', '3o8t', '4aa5', '4e6c', '5wjj', '3fsk', '3hv3', '4eh2', '5xyx', '3hl7', '3gcu', '5mty', '3ody', '3p7a', '2ghl', '5uoj', '3iw7', '1yqj', '3d7z', '3iw6', '3e92', '3fsf', '2yiw', '4ehv', '2zaz', '1zyj', '3gcs', '2i0h', '3fko', '3iph', '3hp5', '5nzz', '4eh5', '2ghm', '3s4q', '3p7b', '6anl', '3hv7', '5eta', '2fsm', '3odz', '4kiq', '1zzl', '3hll', '1yw2', '5tbe', '2gtm', '3hrb', '3lfa', '3fmh', '4lop', '3gcv', '3mh0', '3flz', '3gcq', '3p79', '1zz2', '3mvl', '3e93', '3zsh', '4zth', '3que', '1w7h', '3hv4', '3qud', '3roc', '3nnw', '3py3', '4e8a', '3hv5', '5omh', '1wbt', '3l8s', '2okr', '3l8x', '2bak', '3mgy', '3gc7'}\n",
      "2021-05-17 15:16:03,257 [MainThread  ] [INFO ]  Downloading: 1wbo from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1wbo.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:03,696 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1wbo.pdb\n",
      "2021-05-17 15:16:03,698 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:03,706 [MainThread  ] [INFO ]  Downloading: 5n67 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5n67.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:04,246 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5n67.pdb\n",
      "2021-05-17 15:16:04,249 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:04,272 [MainThread  ] [INFO ]  Downloading: 5o8v from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5o8v.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:04,685 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5o8v.pdb\n",
      "2021-05-17 15:16:04,689 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:04,709 [MainThread  ] [INFO ]  Downloading: 4fa2 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4fa2.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:05,243 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4fa2.pdb\n",
      "2021-05-17 15:16:05,246 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:05,272 [MainThread  ] [INFO ]  Downloading: 1ouy from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1ouy.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:05,739 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1ouy.pdb\n",
      "2021-05-17 15:16:05,740 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:05,748 [MainThread  ] [INFO ]  Downloading: 3nnv from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3nnv.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:06,218 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3nnv.pdb\n",
      "2021-05-17 15:16:06,221 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:06,242 [MainThread  ] [INFO ]  Downloading: 4r3c from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4r3c.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:06,835 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4r3c.pdb\n",
      "2021-05-17 15:16:06,842 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:06,856 [MainThread  ] [INFO ]  Downloading: 1wbv from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1wbv.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:07,285 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1wbv.pdb\n",
      "2021-05-17 15:16:07,289 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:07,309 [MainThread  ] [INFO ]  Downloading: 3o8u from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3o8u.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:07,803 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3o8u.pdb\n",
      "2021-05-17 15:16:07,805 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:07,816 [MainThread  ] [INFO ]  Downloading: 4loq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4loq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:08,838 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4loq.pdb\n",
      "2021-05-17 15:16:08,840 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:08,902 [MainThread  ] [INFO ]  Downloading: 5n63 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5n63.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:09,639 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5n63.pdb\n",
      "2021-05-17 15:16:09,643 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:09,653 [MainThread  ] [INFO ]  Downloading: 3fln from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fln.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:10,316 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fln.pdb\n",
      "2021-05-17 15:16:10,317 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:10,324 [MainThread  ] [INFO ]  Downloading: 5o90 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5o90.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:10,776 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5o90.pdb\n",
      "2021-05-17 15:16:10,779 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:10,795 [MainThread  ] [INFO ]  Downloading: 1kv2 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1kv2.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:11,260 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1kv2.pdb\n",
      "2021-05-17 15:16:11,263 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:11,278 [MainThread  ] [INFO ]  Downloading: 3lfb from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3lfb.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:11,697 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3lfb.pdb\n",
      "2021-05-17 15:16:11,700 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:11,722 [MainThread  ] [INFO ]  Downloading: 4f9w from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4f9w.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:12,526 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4f9w.pdb\n",
      "2021-05-17 15:16:12,529 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:12,561 [MainThread  ] [INFO ]  Downloading: 4aa0 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4aa0.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:13,121 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4aa0.pdb\n",
      "2021-05-17 15:16:13,125 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:13,139 [MainThread  ] [INFO ]  Downloading: 3rin from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3rin.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:13,650 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3rin.pdb\n",
      "2021-05-17 15:16:13,653 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:13,678 [MainThread  ] [INFO ]  Downloading: 3new from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3new.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:14,186 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3new.pdb\n",
      "2021-05-17 15:16:14,189 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:14,212 [MainThread  ] [INFO ]  Downloading: 3zs5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3zs5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:14,757 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3zs5.pdb\n",
      "2021-05-17 15:16:14,760 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:14,773 [MainThread  ] [INFO ]  Downloading: 2oza from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2oza.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:15,341 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2oza.pdb\n",
      "2021-05-17 15:16:15,344 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:15,365 [MainThread  ] [INFO ]  Downloading: 1ouk from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1ouk.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:15,768 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1ouk.pdb\n",
      "2021-05-17 15:16:15,771 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:15,789 [MainThread  ] [INFO ]  Downloading: 3mh1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mh1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:16,292 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mh1.pdb\n",
      "2021-05-17 15:16:16,295 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:16,303 [MainThread  ] [INFO ]  Downloading: 3o8p from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3o8p.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:16,799 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3o8p.pdb\n",
      "2021-05-17 15:16:16,803 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:16,818 [MainThread  ] [INFO ]  Downloading: 1ywr from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1ywr.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:17,267 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1ywr.pdb\n",
      "2021-05-17 15:16:17,271 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:17,293 [MainThread  ] [INFO ]  Downloading: 3obg from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3obg.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:17,738 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3obg.pdb\n",
      "2021-05-17 15:16:17,741 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:17,766 [MainThread  ] [INFO ]  Downloading: 3p7c from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3p7c.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:18,181 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3p7c.pdb\n",
      "2021-05-17 15:16:18,189 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:18,207 [MainThread  ] [INFO ]  Downloading: 3bv3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3bv3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:18,665 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3bv3.pdb\n",
      "2021-05-17 15:16:18,669 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:18,677 [MainThread  ] [INFO ]  Downloading: 5etc from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5etc.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:19,268 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5etc.pdb\n",
      "2021-05-17 15:16:19,269 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:19,280 [MainThread  ] [INFO ]  Downloading: 3p78 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3p78.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:19,692 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3p78.pdb\n",
      "2021-05-17 15:16:19,695 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:19,713 [MainThread  ] [INFO ]  Downloading: 1wbw from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1wbw.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:20,135 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1wbw.pdb\n",
      "2021-05-17 15:16:20,138 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:20,155 [MainThread  ] [INFO ]  Downloading: 3od6 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3od6.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:20,741 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3od6.pdb\n",
      "2021-05-17 15:16:20,743 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:20,753 [MainThread  ] [INFO ]  Downloading: 2zb0 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2zb0.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:21,173 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2zb0.pdb\n",
      "2021-05-17 15:16:21,175 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:21,195 [MainThread  ] [INFO ]  Downloading: 4f9y from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4f9y.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:21,790 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4f9y.pdb\n",
      "2021-05-17 15:16:21,794 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:21,806 [MainThread  ] [INFO ]  Downloading: 1lew from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1lew.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:22,207 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1lew.pdb\n",
      "2021-05-17 15:16:22,211 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:22,228 [MainThread  ] [INFO ]  Downloading: 5tco from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5tco.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:22,653 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5tco.pdb\n",
      "2021-05-17 15:16:22,656 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:22,667 [MainThread  ] [INFO ]  Downloading: 3p5k from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3p5k.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:23,088 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3p5k.pdb\n",
      "2021-05-17 15:16:23,091 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:23,114 [MainThread  ] [INFO ]  Downloading: 2rg5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2rg5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:23,516 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2rg5.pdb\n",
      "2021-05-17 15:16:23,519 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:23,538 [MainThread  ] [INFO ]  Downloading: 2yis from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2yis.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:23,947 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2yis.pdb\n",
      "2021-05-17 15:16:23,950 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:23,967 [MainThread  ] [INFO ]  Downloading: 1bmk from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1bmk.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:24,413 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1bmk.pdb\n",
      "2021-05-17 15:16:24,415 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:24,420 [MainThread  ] [INFO ]  Downloading: 2npq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2npq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:24,862 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2npq.pdb\n",
      "2021-05-17 15:16:24,865 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:24,882 [MainThread  ] [INFO ]  Downloading: 3iw5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3iw5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:25,329 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3iw5.pdb\n",
      "2021-05-17 15:16:25,332 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:25,349 [MainThread  ] [INFO ]  Downloading: 2baq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2baq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:25,806 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2baq.pdb\n",
      "2021-05-17 15:16:25,809 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:25,824 [MainThread  ] [INFO ]  Downloading: 3hp2 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hp2.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:26,237 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hp2.pdb\n",
      "2021-05-17 15:16:26,241 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:26,259 [MainThread  ] [INFO ]  Downloading: 1wfc from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1wfc.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:26,724 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1wfc.pdb\n",
      "2021-05-17 15:16:26,729 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:26,740 [MainThread  ] [INFO ]  Downloading: 3oc1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3oc1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:27,210 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3oc1.pdb\n",
      "2021-05-17 15:16:27,213 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:27,235 [MainThread  ] [INFO ]  Downloading: 4eh4 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4eh4.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:27,782 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh4.pdb\n",
      "2021-05-17 15:16:27,785 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:27,808 [MainThread  ] [INFO ]  Downloading: 3kf7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3kf7.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:28,234 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3kf7.pdb\n",
      "2021-05-17 15:16:28,237 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:28,256 [MainThread  ] [INFO ]  Downloading: 2bal from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2bal.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:28,670 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2bal.pdb\n",
      "2021-05-17 15:16:28,674 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:28,695 [MainThread  ] [INFO ]  Downloading: 5xyy from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5xyy.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:29,132 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5xyy.pdb\n",
      "2021-05-17 15:16:29,135 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:29,160 [MainThread  ] [INFO ]  Downloading: 3flq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3flq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:29,603 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3flq.pdb\n",
      "2021-05-17 15:16:29,607 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:29,629 [MainThread  ] [INFO ]  Downloading: 1w82 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1w82.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:30,128 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1w82.pdb\n",
      "2021-05-17 15:16:30,132 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:30,157 [MainThread  ] [INFO ]  Downloading: 3nww from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3nww.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:30,586 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3nww.pdb\n",
      "2021-05-17 15:16:30,590 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:30,605 [MainThread  ] [INFO ]  Downloading: 3kq7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3kq7.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:31,089 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3kq7.pdb\n",
      "2021-05-17 15:16:31,091 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:31,102 [MainThread  ] [INFO ]  Downloading: 3ha8 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3ha8.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:31,516 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3ha8.pdb\n",
      "2021-05-17 15:16:31,519 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:31,539 [MainThread  ] [INFO ]  Downloading: 4tyh from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4tyh.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:32,200 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4tyh.pdb\n",
      "2021-05-17 15:16:32,203 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:32,242 [MainThread  ] [INFO ]  Downloading: 1m7q from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1m7q.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:32,673 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1m7q.pdb\n",
      "2021-05-17 15:16:32,677 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:32,697 [MainThread  ] [INFO ]  Downloading: 3itz from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3itz.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:33,154 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3itz.pdb\n",
      "2021-05-17 15:16:33,157 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:33,177 [MainThread  ] [INFO ]  Downloading: 3zsi from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3zsi.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:33,723 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3zsi.pdb\n",
      "2021-05-17 15:16:33,726 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:33,755 [MainThread  ] [INFO ]  Downloading: 3fls from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fls.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:34,176 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fls.pdb\n",
      "2021-05-17 15:16:34,181 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:34,199 [MainThread  ] [INFO ]  Downloading: 3s3i from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3s3i.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:34,681 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3s3i.pdb\n",
      "2021-05-17 15:16:34,686 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:34,703 [MainThread  ] [INFO ]  Downloading: 3lfc from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3lfc.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:35,133 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3lfc.pdb\n",
      "2021-05-17 15:16:35,141 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:35,157 [MainThread  ] [INFO ]  Downloading: 3mpt from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mpt.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:35,567 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mpt.pdb\n",
      "2021-05-17 15:16:35,569 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:35,594 [MainThread  ] [INFO ]  Downloading: 4dlj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4dlj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:36,038 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4dlj.pdb\n",
      "2021-05-17 15:16:36,042 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:36,052 [MainThread  ] [INFO ]  Downloading: 3lhj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3lhj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:36,501 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3lhj.pdb\n",
      "2021-05-17 15:16:36,505 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:36,526 [MainThread  ] [INFO ]  Downloading: 3fmn from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fmn.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:36,954 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fmn.pdb\n",
      "2021-05-17 15:16:36,957 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:36,980 [MainThread  ] [INFO ]  Downloading: 5mz3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5mz3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:37,530 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5mz3.pdb\n",
      "2021-05-17 15:16:37,533 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:37,558 [MainThread  ] [INFO ]  Downloading: 1oz1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1oz1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:38,032 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1oz1.pdb\n",
      "2021-05-17 15:16:38,036 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:38,043 [MainThread  ] [INFO ]  Downloading: 4a9y from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4a9y.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:38,603 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4a9y.pdb\n",
      "2021-05-17 15:16:38,607 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:38,632 [MainThread  ] [INFO ]  Downloading: 5lar from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5lar.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:39,173 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5lar.pdb\n",
      "2021-05-17 15:16:39,177 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:39,212 [MainThread  ] [INFO ]  Downloading: 4eh3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4eh3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:39,642 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh3.pdb\n",
      "2021-05-17 15:16:39,646 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:39,661 [MainThread  ] [INFO ]  Downloading: 1r39 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1r39.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:40,109 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1r39.pdb\n",
      "2021-05-17 15:16:40,113 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:40,131 [MainThread  ] [INFO ]  Downloading: 3mw1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mw1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:40,595 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mw1.pdb\n",
      "2021-05-17 15:16:40,600 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:40,618 [MainThread  ] [INFO ]  Downloading: 3k3i from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3k3i.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:41,040 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3k3i.pdb\n",
      "2021-05-17 15:16:41,043 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:41,060 [MainThread  ] [INFO ]  Downloading: 3dt1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3dt1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:41,505 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3dt1.pdb\n",
      "2021-05-17 15:16:41,509 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:41,526 [MainThread  ] [INFO ]  Downloading: 2onl from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2onl.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:42,241 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2onl.pdb\n",
      "2021-05-17 15:16:42,244 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:42,294 [MainThread  ] [INFO ]  Downloading: 1bl7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1bl7.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:42,749 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1bl7.pdb\n",
      "2021-05-17 15:16:42,755 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:42,770 [MainThread  ] [INFO ]  Downloading: 3fmj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fmj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:43,213 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fmj.pdb\n",
      "2021-05-17 15:16:43,217 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:43,225 [MainThread  ] [INFO ]  Downloading: 3hec from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hec.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:43,623 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hec.pdb\n",
      "2021-05-17 15:16:43,627 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:43,652 [MainThread  ] [INFO ]  Downloading: 3hv6 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hv6.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:44,078 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hv6.pdb\n",
      "2021-05-17 15:16:44,082 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:44,100 [MainThread  ] [INFO ]  Downloading: 4kip from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4kip.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:44,621 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4kip.pdb\n",
      "2021-05-17 15:16:44,624 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:44,649 [MainThread  ] [INFO ]  Downloading: 4loo from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4loo.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:45,192 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4loo.pdb\n",
      "2021-05-17 15:16:45,196 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:45,230 [MainThread  ] [INFO ]  Downloading: 3fkn from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fkn.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:45,685 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fkn.pdb\n",
      "2021-05-17 15:16:45,688 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:45,709 [MainThread  ] [INFO ]  Downloading: 3iw8 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3iw8.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:46,156 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3iw8.pdb\n",
      "2021-05-17 15:16:46,159 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:46,170 [MainThread  ] [INFO ]  Downloading: 1a9u from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1a9u.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:46,617 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1a9u.pdb\n",
      "2021-05-17 15:16:46,620 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:46,640 [MainThread  ] [INFO ]  Downloading: 3fc1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fc1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:47,177 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fc1.pdb\n",
      "2021-05-17 15:16:47,178 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:47,184 [MainThread  ] [INFO ]  Downloading: 3mvm from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mvm.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:47,741 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mvm.pdb\n",
      "2021-05-17 15:16:47,744 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:47,762 [MainThread  ] [INFO ]  Downloading: 3uvq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3uvq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:48,298 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3uvq.pdb\n",
      "2021-05-17 15:16:48,302 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:48,319 [MainThread  ] [INFO ]  Downloading: 4eh9 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4eh9.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:48,809 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh9.pdb\n",
      "2021-05-17 15:16:48,812 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:48,836 [MainThread  ] [INFO ]  Downloading: 3ds6 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3ds6.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:49,659 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3ds6.pdb\n",
      "2021-05-17 15:16:49,662 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:49,700 [MainThread  ] [INFO ]  Downloading: 1di9 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1di9.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:50,136 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1di9.pdb\n",
      "2021-05-17 15:16:50,140 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:50,162 [MainThread  ] [INFO ]  Downloading: 3tg1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3tg1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:50,747 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3tg1.pdb\n",
      "2021-05-17 15:16:50,755 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:50,783 [MainThread  ] [INFO ]  Downloading: 3zya from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3zya.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:51,474 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3zya.pdb\n",
      "2021-05-17 15:16:51,477 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:51,505 [MainThread  ] [INFO ]  Downloading: 4l8m from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4l8m.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:51,949 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4l8m.pdb\n",
      "2021-05-17 15:16:51,952 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:51,971 [MainThread  ] [INFO ]  Downloading: 4dli from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4dli.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:52,427 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4dli.pdb\n",
      "2021-05-17 15:16:52,428 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:52,434 [MainThread  ] [INFO ]  Downloading: 2lgc from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2lgc.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:53,790 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2lgc.pdb\n",
      "2021-05-17 15:16:53,794 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:53,862 [MainThread  ] [INFO ]  Downloading: 3flw from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3flw.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:54,381 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3flw.pdb\n",
      "2021-05-17 15:16:54,384 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:54,401 [MainThread  ] [INFO ]  Downloading: 1w84 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1w84.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:54,833 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1w84.pdb\n",
      "2021-05-17 15:16:54,837 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:54,864 [MainThread  ] [INFO ]  Downloading: 3c5u from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3c5u.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:55,305 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3c5u.pdb\n",
      "2021-05-17 15:16:55,309 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:55,325 [MainThread  ] [INFO ]  Downloading: 3ctq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3ctq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:55,903 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3ctq.pdb\n",
      "2021-05-17 15:16:55,905 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:55,912 [MainThread  ] [INFO ]  Downloading: 3fly from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fly.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:56,360 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fly.pdb\n",
      "2021-05-17 15:16:56,364 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:56,382 [MainThread  ] [INFO ]  Downloading: 3fml from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fml.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:56,844 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fml.pdb\n",
      "2021-05-17 15:16:56,849 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:56,868 [MainThread  ] [INFO ]  Downloading: 3u8w from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3u8w.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:57,331 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3u8w.pdb\n",
      "2021-05-17 15:16:57,334 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:57,342 [MainThread  ] [INFO ]  Downloading: 2fst from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2fst.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:57,855 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2fst.pdb\n",
      "2021-05-17 15:16:57,859 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:57,897 [MainThread  ] [INFO ]  Downloading: 5mtx from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5mtx.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:16:58,325 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5mtx.pdb\n",
      "2021-05-17 15:16:58,329 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:58,346 [MainThread  ] [INFO ]  Downloading: 5n66 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5n66.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:58,867 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5n66.pdb\n",
      "2021-05-17 15:16:58,870 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:58,893 [MainThread  ] [INFO ]  Downloading: 2fso from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2fso.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:59,321 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2fso.pdb\n",
      "2021-05-17 15:16:59,325 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:59,343 [MainThread  ] [INFO ]  Downloading: 2gfs from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2gfs.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:16:59,777 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2gfs.pdb\n",
      "2021-05-17 15:16:59,780 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:16:59,798 [MainThread  ] [INFO ]  Downloading: 5eti from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5eti.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:00,231 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5eti.pdb\n",
      "2021-05-17 15:17:00,234 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:00,243 [MainThread  ] [INFO ]  Downloading: 3mpa from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mpa.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:00,675 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mpa.pdb\n",
      "2021-05-17 15:17:00,678 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:00,701 [MainThread  ] [INFO ]  Downloading: 3heg from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3heg.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:01,122 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3heg.pdb\n",
      "2021-05-17 15:17:01,125 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:01,142 [MainThread  ] [INFO ]  Downloading: 3nnu from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3nnu.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:01,590 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3nnu.pdb\n",
      "2021-05-17 15:17:01,593 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:01,610 [MainThread  ] [INFO ]  Downloading: 2y8o from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2y8o.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:02,160 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2y8o.pdb\n",
      "2021-05-17 15:17:02,164 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:02,190 [MainThread  ] [INFO ]  Downloading: 2qd9 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2qd9.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:02,621 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2qd9.pdb\n",
      "2021-05-17 15:17:02,625 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:02,647 [MainThread  ] [INFO ]  Downloading: 3zsg from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3zsg.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:03,179 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3zsg.pdb\n",
      "2021-05-17 15:17:03,182 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:03,210 [MainThread  ] [INFO ]  Downloading: 5n68 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5n68.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:03,789 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5n68.pdb\n",
      "2021-05-17 15:17:03,791 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:03,812 [MainThread  ] [INFO ]  Downloading: 1r3c from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1r3c.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:04,222 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1r3c.pdb\n",
      "2021-05-17 15:17:04,225 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:04,244 [MainThread  ] [INFO ]  Downloading: 2puu from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2puu.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:04,660 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2puu.pdb\n",
      "2021-05-17 15:17:04,663 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:04,680 [MainThread  ] [INFO ]  Downloading: 5etf from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5etf.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:05,111 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5etf.pdb\n",
      "2021-05-17 15:17:05,115 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:05,133 [MainThread  ] [INFO ]  Downloading: 3p4k from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3p4k.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:05,587 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3p4k.pdb\n",
      "2021-05-17 15:17:05,591 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:05,609 [MainThread  ] [INFO ]  Downloading: 3lfd from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3lfd.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:06,169 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3lfd.pdb\n",
      "2021-05-17 15:17:06,174 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:06,192 [MainThread  ] [INFO ]  Downloading: 5ml5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5ml5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:06,738 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5ml5.pdb\n",
      "2021-05-17 15:17:06,746 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:06,770 [MainThread  ] [INFO ]  Downloading: 5n65 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5n65.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:07,280 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5n65.pdb\n",
      "2021-05-17 15:17:07,284 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:07,309 [MainThread  ] [INFO ]  Downloading: 2yix from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2yix.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:07,723 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2yix.pdb\n",
      "2021-05-17 15:17:07,727 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:07,744 [MainThread  ] [INFO ]  Downloading: 1w83 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1w83.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:08,320 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1w83.pdb\n",
      "2021-05-17 15:17:08,323 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:08,331 [MainThread  ] [INFO ]  Downloading: 3uvr from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3uvr.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:08,751 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3uvr.pdb\n",
      "2021-05-17 15:17:08,755 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:08,771 [MainThread  ] [INFO ]  Downloading: 4eh7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4eh7.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:09,217 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh7.pdb\n",
      "2021-05-17 15:17:09,221 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:09,245 [MainThread  ] [INFO ]  Downloading: 4kin from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4kin.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:09,984 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4kin.pdb\n",
      "2021-05-17 15:17:09,987 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:10,026 [MainThread  ] [INFO ]  Downloading: 3fmm from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fmm.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:10,455 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fmm.pdb\n",
      "2021-05-17 15:17:10,460 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:10,484 [MainThread  ] [INFO ]  Downloading: 3mh3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mh3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:10,906 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mh3.pdb\n",
      "2021-05-17 15:17:10,911 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:10,932 [MainThread  ] [INFO ]  Downloading: 3nnx from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3nnx.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:11,381 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3nnx.pdb\n",
      "2021-05-17 15:17:11,384 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:11,403 [MainThread  ] [INFO ]  Downloading: 5n64 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5n64.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:11,893 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5n64.pdb\n",
      "2021-05-17 15:17:11,897 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:11,920 [MainThread  ] [INFO ]  Downloading: 3gfe from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3gfe.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:12,352 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3gfe.pdb\n",
      "2021-05-17 15:17:12,356 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:12,376 [MainThread  ] [INFO ]  Downloading: 5omg from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5omg.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:12,837 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5omg.pdb\n",
      "2021-05-17 15:17:12,840 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:12,860 [MainThread  ] [INFO ]  Downloading: 2baj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2baj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:13,263 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2baj.pdb\n",
      "2021-05-17 15:17:13,269 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:13,283 [MainThread  ] [INFO ]  Downloading: 3fmk from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fmk.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:13,681 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fmk.pdb\n",
      "2021-05-17 15:17:13,685 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:13,705 [MainThread  ] [INFO ]  Downloading: 2zb1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2zb1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:14,129 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2zb1.pdb\n",
      "2021-05-17 15:17:14,132 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:14,144 [MainThread  ] [INFO ]  Downloading: 3hvc from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hvc.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:14,556 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hvc.pdb\n",
      "2021-05-17 15:17:14,564 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:14,578 [MainThread  ] [INFO ]  Downloading: 1kv1 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1kv1.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:15,017 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1kv1.pdb\n",
      "2021-05-17 15:17:15,020 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:15,038 [MainThread  ] [INFO ]  Downloading: 3d83 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3d83.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:15,485 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3d83.pdb\n",
      "2021-05-17 15:17:15,488 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:15,507 [MainThread  ] [INFO ]  Downloading: 3fi4 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fi4.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:15,949 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fi4.pdb\n",
      "2021-05-17 15:17:15,953 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:15,975 [MainThread  ] [INFO ]  Downloading: 3fkl from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fkl.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:16,397 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fkl.pdb\n",
      "2021-05-17 15:17:16,398 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:16,406 [MainThread  ] [INFO ]  Downloading: 3gi3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3gi3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:16,871 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3gi3.pdb\n",
      "2021-05-17 15:17:16,872 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:16,880 [MainThread  ] [INFO ]  Downloading: 4eh6 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4eh6.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:17,290 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh6.pdb\n",
      "2021-05-17 15:17:17,292 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:17,300 [MainThread  ] [INFO ]  Downloading: 3fl4 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fl4.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:17,737 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fl4.pdb\n",
      "2021-05-17 15:17:17,741 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:17,766 [MainThread  ] [INFO ]  Downloading: 3lff from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3lff.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:18,178 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3lff.pdb\n",
      "2021-05-17 15:17:18,182 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:18,201 [MainThread  ] [INFO ]  Downloading: 3k3j from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3k3j.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:18,623 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3k3j.pdb\n",
      "2021-05-17 15:17:18,627 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:18,643 [MainThread  ] [INFO ]  Downloading: 3huc from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3huc.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:19,061 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3huc.pdb\n",
      "2021-05-17 15:17:19,064 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:19,081 [MainThread  ] [INFO ]  Downloading: 3obj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3obj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:19,517 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3obj.pdb\n",
      "2021-05-17 15:17:19,519 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:19,528 [MainThread  ] [INFO ]  Downloading: 3uvp from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3uvp.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:19,941 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3uvp.pdb\n",
      "2021-05-17 15:17:19,944 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:19,970 [MainThread  ] [INFO ]  Downloading: 3pg3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3pg3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:20,429 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3pg3.pdb\n",
      "2021-05-17 15:17:20,430 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:20,438 [MainThread  ] [INFO ]  Downloading: 1ian from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1ian.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:20,707 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1ian.pdb\n",
      "2021-05-17 15:17:20,710 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:20,717 [MainThread  ] [INFO ]  Downloading: 3bv2 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3bv2.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:21,132 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3bv2.pdb\n",
      "2021-05-17 15:17:21,135 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:21,158 [MainThread  ] [INFO ]  Downloading: 4aac from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4aac.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:21,693 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4aac.pdb\n",
      "2021-05-17 15:17:21,696 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:21,720 [MainThread  ] [INFO ]  Downloading: 1wbn from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1wbn.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:22,142 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1wbn.pdb\n",
      "2021-05-17 15:17:22,144 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:22,163 [MainThread  ] [INFO ]  Downloading: 3lfe from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3lfe.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:22,599 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3lfe.pdb\n",
      "2021-05-17 15:17:22,603 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:22,616 [MainThread  ] [INFO ]  Downloading: 1wbs from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1wbs.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:23,046 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1wbs.pdb\n",
      "2021-05-17 15:17:23,048 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:23,061 [MainThread  ] [INFO ]  Downloading: 1ove from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1ove.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:23,506 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1ove.pdb\n",
      "2021-05-17 15:17:23,511 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:23,533 [MainThread  ] [INFO ]  Downloading: 3mh2 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mh2.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:23,966 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mh2.pdb\n",
      "2021-05-17 15:17:23,969 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:23,992 [MainThread  ] [INFO ]  Downloading: 4eh8 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4eh8.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:24,390 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh8.pdb\n",
      "2021-05-17 15:17:24,393 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:24,402 [MainThread  ] [INFO ]  Downloading: 2fsl from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2fsl.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:24,826 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2fsl.pdb\n",
      "2021-05-17 15:17:24,829 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:24,847 [MainThread  ] [INFO ]  Downloading: 5o8u from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5o8u.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:25,261 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5o8u.pdb\n",
      "2021-05-17 15:17:25,264 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:25,280 [MainThread  ] [INFO ]  Downloading: 2ewa from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2ewa.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:25,710 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2ewa.pdb\n",
      "2021-05-17 15:17:25,714 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:25,736 [MainThread  ] [INFO ]  Downloading: 1lez from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1lez.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:26,174 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1lez.pdb\n",
      "2021-05-17 15:17:26,178 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:26,197 [MainThread  ] [INFO ]  Downloading: 4e5a from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4e5a.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:26,671 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4e5a.pdb\n",
      "2021-05-17 15:17:26,675 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:26,698 [MainThread  ] [INFO ]  Downloading: 3bx5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3bx5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:27,225 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3bx5.pdb\n",
      "2021-05-17 15:17:27,229 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:27,250 [MainThread  ] [INFO ]  Downloading: 3ocg from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3ocg.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:27,737 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3ocg.pdb\n",
      "2021-05-17 15:17:27,740 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:27,757 [MainThread  ] [INFO ]  Downloading: 4geo from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4geo.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:28,421 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4geo.pdb\n",
      "2021-05-17 15:17:28,422 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:28,428 [MainThread  ] [INFO ]  Downloading: 2rg6 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2rg6.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:28,958 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2rg6.pdb\n",
      "2021-05-17 15:17:28,962 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:28,972 [MainThread  ] [INFO ]  Downloading: 3gcp from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3gcp.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:29,463 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3gcp.pdb\n",
      "2021-05-17 15:17:29,465 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:29,475 [MainThread  ] [INFO ]  Downloading: 3oef from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3oef.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:30,018 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3oef.pdb\n",
      "2021-05-17 15:17:30,019 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:30,039 [MainThread  ] [INFO ]  Downloading: 3hub from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hub.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:30,596 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hub.pdb\n",
      "2021-05-17 15:17:30,597 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:30,604 [MainThread  ] [INFO ]  Downloading: 4ewq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4ewq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:31,061 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4ewq.pdb\n",
      "2021-05-17 15:17:31,062 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:31,077 [MainThread  ] [INFO ]  Downloading: 1bl6 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1bl6.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:31,776 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1bl6.pdb\n",
      "2021-05-17 15:17:31,779 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:31,797 [MainThread  ] [INFO ]  Downloading: 4e6a from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4e6a.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:32,287 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4e6a.pdb\n",
      "2021-05-17 15:17:32,291 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:32,312 [MainThread  ] [INFO ]  Downloading: 4aa4 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4aa4.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:32,974 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4aa4.pdb\n",
      "2021-05-17 15:17:32,976 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:32,988 [MainThread  ] [INFO ]  Downloading: 2gtn from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2gtn.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:33,466 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2gtn.pdb\n",
      "2021-05-17 15:17:33,469 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:33,487 [MainThread  ] [INFO ]  Downloading: 4e5b from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4e5b.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:33,951 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4e5b.pdb\n",
      "2021-05-17 15:17:33,955 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:33,971 [MainThread  ] [INFO ]  Downloading: 4ka3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4ka3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:34,514 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4ka3.pdb\n",
      "2021-05-17 15:17:34,517 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:34,542 [MainThread  ] [INFO ]  Downloading: 3o8t from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3o8t.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:35,150 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3o8t.pdb\n",
      "2021-05-17 15:17:35,158 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:35,169 [MainThread  ] [INFO ]  Downloading: 4aa5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4aa5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:35,702 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4aa5.pdb\n",
      "2021-05-17 15:17:35,705 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:35,728 [MainThread  ] [INFO ]  Downloading: 4e6c from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4e6c.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:36,181 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4e6c.pdb\n",
      "2021-05-17 15:17:36,185 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:36,201 [MainThread  ] [INFO ]  Downloading: 5wjj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5wjj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:36,742 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5wjj.pdb\n",
      "2021-05-17 15:17:36,746 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:36,772 [MainThread  ] [INFO ]  Downloading: 3fsk from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fsk.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:37,212 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fsk.pdb\n",
      "2021-05-17 15:17:37,217 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:37,241 [MainThread  ] [INFO ]  Downloading: 3hv3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hv3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:37,648 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hv3.pdb\n",
      "2021-05-17 15:17:37,651 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:37,666 [MainThread  ] [INFO ]  Downloading: 4eh2 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4eh2.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:38,087 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh2.pdb\n",
      "2021-05-17 15:17:38,090 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:38,107 [MainThread  ] [INFO ]  Downloading: 5xyx from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5xyx.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:38,544 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5xyx.pdb\n",
      "2021-05-17 15:17:38,548 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:38,578 [MainThread  ] [INFO ]  Downloading: 3hl7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hl7.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:39,015 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hl7.pdb\n",
      "2021-05-17 15:17:39,018 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:39,036 [MainThread  ] [INFO ]  Downloading: 3gcu from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3gcu.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:39,575 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3gcu.pdb\n",
      "2021-05-17 15:17:39,578 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:39,596 [MainThread  ] [INFO ]  Downloading: 5mty from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5mty.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:40,024 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5mty.pdb\n",
      "2021-05-17 15:17:40,028 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:40,049 [MainThread  ] [INFO ]  Downloading: 3ody from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3ody.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:40,534 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3ody.pdb\n",
      "2021-05-17 15:17:40,542 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:40,572 [MainThread  ] [INFO ]  Downloading: 3p7a from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3p7a.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:40,996 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3p7a.pdb\n",
      "2021-05-17 15:17:41,001 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:41,018 [MainThread  ] [INFO ]  Downloading: 2ghl from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2ghl.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:41,427 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2ghl.pdb\n",
      "2021-05-17 15:17:41,428 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:41,435 [MainThread  ] [INFO ]  Downloading: 5uoj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5uoj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:41,869 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5uoj.pdb\n",
      "2021-05-17 15:17:41,872 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:41,891 [MainThread  ] [INFO ]  Downloading: 3iw7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3iw7.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:42,303 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3iw7.pdb\n",
      "2021-05-17 15:17:42,307 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:42,335 [MainThread  ] [INFO ]  Downloading: 1yqj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1yqj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:42,812 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1yqj.pdb\n",
      "2021-05-17 15:17:42,816 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:42,823 [MainThread  ] [INFO ]  Downloading: 3d7z from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3d7z.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:43,255 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3d7z.pdb\n",
      "2021-05-17 15:17:43,259 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:43,279 [MainThread  ] [INFO ]  Downloading: 3iw6 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3iw6.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:43,694 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3iw6.pdb\n",
      "2021-05-17 15:17:43,698 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:43,716 [MainThread  ] [INFO ]  Downloading: 3e92 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3e92.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:44,163 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3e92.pdb\n",
      "2021-05-17 15:17:44,166 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:44,186 [MainThread  ] [INFO ]  Downloading: 3fsf from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fsf.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:44,612 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fsf.pdb\n",
      "2021-05-17 15:17:44,615 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:44,632 [MainThread  ] [INFO ]  Downloading: 2yiw from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2yiw.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:45,104 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2yiw.pdb\n",
      "2021-05-17 15:17:45,107 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:45,127 [MainThread  ] [INFO ]  Downloading: 4ehv from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4ehv.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:45,620 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4ehv.pdb\n",
      "2021-05-17 15:17:45,623 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:45,647 [MainThread  ] [INFO ]  Downloading: 2zaz from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2zaz.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:46,120 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2zaz.pdb\n",
      "2021-05-17 15:17:46,124 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:46,142 [MainThread  ] [INFO ]  Downloading: 1zyj from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1zyj.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:46,554 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1zyj.pdb\n",
      "2021-05-17 15:17:46,557 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:46,573 [MainThread  ] [INFO ]  Downloading: 3gcs from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3gcs.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:47,018 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3gcs.pdb\n",
      "2021-05-17 15:17:47,021 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:47,039 [MainThread  ] [INFO ]  Downloading: 2i0h from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2i0h.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:47,466 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2i0h.pdb\n",
      "2021-05-17 15:17:47,469 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:47,488 [MainThread  ] [INFO ]  Downloading: 3fko from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fko.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:47,885 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fko.pdb\n",
      "2021-05-17 15:17:47,889 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:47,912 [MainThread  ] [INFO ]  Downloading: 3iph from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3iph.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:48,343 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3iph.pdb\n",
      "2021-05-17 15:17:48,347 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:48,367 [MainThread  ] [INFO ]  Downloading: 3hp5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hp5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:48,809 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hp5.pdb\n",
      "2021-05-17 15:17:48,813 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:48,837 [MainThread  ] [INFO ]  Downloading: 5nzz from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5nzz.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:50,185 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5nzz.pdb\n",
      "2021-05-17 15:17:50,188 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:50,222 [MainThread  ] [INFO ]  Downloading: 4eh5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4eh5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:50,660 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh5.pdb\n",
      "2021-05-17 15:17:50,668 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:50,677 [MainThread  ] [INFO ]  Downloading: 2ghm from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2ghm.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:51,090 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2ghm.pdb\n",
      "2021-05-17 15:17:51,093 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:51,111 [MainThread  ] [INFO ]  Downloading: 3s4q from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3s4q.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:51,556 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3s4q.pdb\n",
      "2021-05-17 15:17:51,560 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:51,579 [MainThread  ] [INFO ]  Downloading: 3p7b from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3p7b.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:51,989 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3p7b.pdb\n",
      "2021-05-17 15:17:51,992 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:52,010 [MainThread  ] [INFO ]  Downloading: 6anl from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb6anl.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:52,560 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/6anl.pdb\n",
      "2021-05-17 15:17:52,564 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:52,593 [MainThread  ] [INFO ]  Downloading: 3hv7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hv7.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:53,008 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hv7.pdb\n",
      "2021-05-17 15:17:53,012 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:53,036 [MainThread  ] [INFO ]  Downloading: 5eta from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5eta.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:53,676 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5eta.pdb\n",
      "2021-05-17 15:17:53,680 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:53,716 [MainThread  ] [INFO ]  Downloading: 2fsm from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2fsm.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:54,131 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2fsm.pdb\n",
      "2021-05-17 15:17:54,134 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:54,152 [MainThread  ] [INFO ]  Downloading: 3odz from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3odz.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:54,670 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3odz.pdb\n",
      "2021-05-17 15:17:54,675 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:54,699 [MainThread  ] [INFO ]  Downloading: 4kiq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4kiq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:55,322 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4kiq.pdb\n",
      "2021-05-17 15:17:55,323 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:55,351 [MainThread  ] [INFO ]  Downloading: 1zzl from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1zzl.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:55,771 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1zzl.pdb\n",
      "2021-05-17 15:17:55,774 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:55,793 [MainThread  ] [INFO ]  Downloading: 3hll from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hll.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:56,255 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hll.pdb\n",
      "2021-05-17 15:17:56,258 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:56,266 [MainThread  ] [INFO ]  Downloading: 1yw2 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1yw2.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:56,742 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1yw2.pdb\n",
      "2021-05-17 15:17:56,745 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:56,762 [MainThread  ] [INFO ]  Downloading: 5tbe from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5tbe.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:57,187 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5tbe.pdb\n",
      "2021-05-17 15:17:57,190 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:57,213 [MainThread  ] [INFO ]  Downloading: 2gtm from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2gtm.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:17:57,653 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2gtm.pdb\n",
      "2021-05-17 15:17:57,657 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:57,674 [MainThread  ] [INFO ]  Downloading: 3hrb from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hrb.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:58,158 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hrb.pdb\n",
      "2021-05-17 15:17:58,161 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:58,185 [MainThread  ] [INFO ]  Downloading: 3lfa from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3lfa.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:58,587 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3lfa.pdb\n",
      "2021-05-17 15:17:58,590 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:58,607 [MainThread  ] [INFO ]  Downloading: 3fmh from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3fmh.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:59,035 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3fmh.pdb\n",
      "2021-05-17 15:17:59,038 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:59,062 [MainThread  ] [INFO ]  Downloading: 4lop from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4lop.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:17:59,829 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4lop.pdb\n",
      "2021-05-17 15:17:59,832 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:17:59,894 [MainThread  ] [INFO ]  Downloading: 3gcv from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3gcv.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:00,312 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3gcv.pdb\n",
      "2021-05-17 15:18:00,317 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:00,335 [MainThread  ] [INFO ]  Downloading: 3mh0 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mh0.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:00,769 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mh0.pdb\n",
      "2021-05-17 15:18:00,772 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:00,794 [MainThread  ] [INFO ]  Downloading: 3flz from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3flz.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:01,210 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3flz.pdb\n",
      "2021-05-17 15:18:01,214 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:01,233 [MainThread  ] [INFO ]  Downloading: 3gcq from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3gcq.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:01,685 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3gcq.pdb\n",
      "2021-05-17 15:18:01,689 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:01,707 [MainThread  ] [INFO ]  Downloading: 3p79 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3p79.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:02,126 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3p79.pdb\n",
      "2021-05-17 15:18:02,128 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:02,147 [MainThread  ] [INFO ]  Downloading: 1zz2 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1zz2.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:02,576 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1zz2.pdb\n",
      "2021-05-17 15:18:02,580 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:02,599 [MainThread  ] [INFO ]  Downloading: 3mvl from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mvl.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:03,139 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mvl.pdb\n",
      "2021-05-17 15:18:03,144 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:03,155 [MainThread  ] [INFO ]  Downloading: 3e93 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3e93.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:03,571 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3e93.pdb\n",
      "2021-05-17 15:18:03,575 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:03,593 [MainThread  ] [INFO ]  Downloading: 3zsh from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3zsh.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:04,104 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3zsh.pdb\n",
      "2021-05-17 15:18:04,106 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:04,132 [MainThread  ] [INFO ]  Downloading: 4zth from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4zth.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:04,674 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4zth.pdb\n",
      "2021-05-17 15:18:04,678 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:04,693 [MainThread  ] [INFO ]  Downloading: 3que from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3que.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:05,201 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3que.pdb\n",
      "2021-05-17 15:18:05,204 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:05,226 [MainThread  ] [INFO ]  Downloading: 1w7h from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1w7h.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:05,741 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1w7h.pdb\n",
      "2021-05-17 15:18:05,749 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:05,759 [MainThread  ] [INFO ]  Downloading: 3hv4 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hv4.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:06,315 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hv4.pdb\n",
      "2021-05-17 15:18:06,319 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:06,330 [MainThread  ] [INFO ]  Downloading: 3qud from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3qud.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:06,793 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3qud.pdb\n",
      "2021-05-17 15:18:06,795 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:06,814 [MainThread  ] [INFO ]  Downloading: 3roc from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3roc.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:07,342 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3roc.pdb\n",
      "2021-05-17 15:18:07,346 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:07,371 [MainThread  ] [INFO ]  Downloading: 3nnw from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3nnw.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:07,824 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3nnw.pdb\n",
      "2021-05-17 15:18:07,828 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:07,848 [MainThread  ] [INFO ]  Downloading: 3py3 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3py3.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:08,450 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3py3.pdb\n",
      "2021-05-17 15:18:08,453 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:08,486 [MainThread  ] [INFO ]  Downloading: 4e8a from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4e8a.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:08,938 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/4e8a.pdb\n",
      "2021-05-17 15:18:08,942 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:08,959 [MainThread  ] [INFO ]  Downloading: 3hv5 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3hv5.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:09,636 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3hv5.pdb\n",
      "2021-05-17 15:18:09,640 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:09,651 [MainThread  ] [INFO ]  Downloading: 5omh from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5omh.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:10,127 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/5omh.pdb\n",
      "2021-05-17 15:18:10,130 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:10,148 [MainThread  ] [INFO ]  Downloading: 1wbt from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb1wbt.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:10,567 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/1wbt.pdb\n",
      "2021-05-17 15:18:10,570 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:10,595 [MainThread  ] [INFO ]  Downloading: 3l8s from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3l8s.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:11,137 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3l8s.pdb\n",
      "2021-05-17 15:18:11,140 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:11,156 [MainThread  ] [INFO ]  Downloading: 2okr from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2okr.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:11,760 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2okr.pdb\n",
      "2021-05-17 15:18:11,762 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:11,776 [MainThread  ] [INFO ]  Downloading: 3l8x from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3l8x.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:12,275 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3l8x.pdb\n",
      "2021-05-17 15:18:12,280 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:12,297 [MainThread  ] [INFO ]  Downloading: 2bak from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2bak.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:12,734 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/2bak.pdb\n",
      "2021-05-17 15:18:12,735 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:12,741 [MainThread  ] [INFO ]  Downloading: 3mgy from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3mgy.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:13,349 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3mgy.pdb\n",
      "2021-05-17 15:18:13,352 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:13,362 [MainThread  ] [INFO ]  Downloading: 3gc7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb3gc7.ent\n",
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/urllib3/connectionpool.py:1020: InsecureRequestWarning: Unverified HTTPS request is being made to host 'www.ebi.ac.uk'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings\n",
      "  InsecureRequestWarning,\n",
      "2021-05-17 15:18:14,019 [MainThread  ] [INFO ]  Writting pdb to: ef39c5c6-6878-49ff-8a15-b88b851253bd/3gc7.pdb\n",
      "2021-05-17 15:18:14,027 [MainThread  ] [INFO ]  Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM']\n",
      "2021-05-17 15:18:14,290 [MainThread  ] [INFO ]  Adding:\n",
      "2021-05-17 15:18:14,291 [MainThread  ] [INFO ]  ['/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/1a9u.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/1bl6.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/1bl7.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/1bmk.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/1di9.pdb', 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'/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4e6a.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4e6c.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4e8a.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh2.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh3.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh4.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh5.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh6.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh7.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh8.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4eh9.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4ehv.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4ewq.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4f9w.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4f9y.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4fa2.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4geo.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4ka3.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4kin.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4kip.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4kiq.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4l8m.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4loo.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4lop.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4loq.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4r3c.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4tyh.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/4zth.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5eta.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5etc.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5etf.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5eti.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5lar.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5ml5.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5mtx.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5mty.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5mz3.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5n63.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5n64.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5n65.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5n66.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5n67.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5n68.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5nzz.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5o8u.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5o8v.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5o90.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5omg.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5omh.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5tbe.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5tco.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5uoj.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5wjj.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5xyx.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/5xyy.pdb', '/home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/ef39c5c6-6878-49ff-8a15-b88b851253bd/6anl.pdb']\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:14,293 [MainThread  ] [INFO ]  to: /home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/pdb_cluster.zip\n",
      "2021-05-17 15:18:14,322 [MainThread  ] [INFO ]  Removed temporary folder: ef39c5c6-6878-49ff-8a15-b88b851253bd\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_io.api.pdb_cluster_zip import pdb_cluster_zip\n",
    "\n",
    "pdb_cluster = \"pdb_cluster.zip\"\n",
    "prop = {\n",
    "    \"pdb_code\": pdb_code,\n",
    "    \"filter\": [\"ATOM\", \"HETATM\"],\n",
    "    \"cluster\": 90\n",
    "}\n",
    "\n",
    "pdb_cluster_zip(output_pdb_zip_path = pdb_cluster,\n",
    "            properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"bindingsite\"></a>\n",
    "### Extracting the Cluster90 Binding Site(s)  \n",
    "Extracting the protein binding site(s) from the **Cluster90** collection. There are two ways in which the **Cluster90 Binding Site** can be used:\n",
    "\n",
    "- **With information about the ligand**: In this particular example we already know the **ligand** we want to dock, and also that the **PDB database** contain an **experimental structure** where the **ligand** was solved in **complex** with our protein of interest (**p38-α Tyrosine kinase**). In that case, the **ligand id** can be used to guide the **binding site** tool. <br><br>\n",
    "- **Without information about the ligand**: If the docking study starts from a **protein receptor** with no information about the **binding site** or any known **protein-ligand complex**, the **binding site** tool can not be guided. Still, the tool should be able to extract **binding site(s)** information from **similar proteins** solved with **small molecules** attached (if any).<br><br>\n",
    "\n",
    "This example is using the **ligand id** to guide the **binding site tool**, but we invite you to try and explore the differences in the output removing this **input information** (ligand property in the next building block).\n",
    "\n",
    "The **Cluster90 binding site** tool is internally running **sequence alignments** to structurally **superpose** the structures contained in the **Cluster90 collection** and extract the **residue numbering** corresponding to the **binding site** residues. Thus, **sequence alignment parameters** can be changed using building block input properties. In this example, we have chosen the well-known **blosum62** substitution matrix, with a **penalty** for opening a gap of -10.0, and a **penalty** to extend a gap of -0.5. The total number of **superimposed ligands** to be extracted from the cluster is limited at 15, and the **cut-off distance** around the ligand atoms to consider a residue to be part of a **binding site** is fixed at 5 Ångstroms."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/anaconda3/envs/biobb_VS_tutorial/lib/python3.7/site-packages/Bio/SubsMat/__init__.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.\n",
      "  BiopythonDeprecationWarning,\n",
      "2021-05-17 15:18:30,064 [MainThread  ] [INFO ]  Loading input PDB structure pdb_protein.pdb\n",
      "2021-05-17 15:18:30,142 [MainThread  ] [INFO ]  Found 329 residues in pdb_protein.pdb\n",
      "2021-05-17 15:18:30,144 [MainThread  ] [INFO ]  Creating 224c5ac9-25fc-4b30-a3b5-de67eeae6bef temporary folder\n",
      "2021-05-17 15:18:30,429 [MainThread  ] [INFO ]  Extracting: /home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/pdb_cluster.zip\n",
      "2021-05-17 15:18:30,430 [MainThread  ] [INFO ]  to:\n",
      "2021-05-17 15:18:30,431 [MainThread  ] [INFO ]  ['224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1a9u.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1bl6.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1bl7.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1bmk.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1di9.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1ian.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1kv1.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1kv2.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1lew.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1lez.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1m7q.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1ouk.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1ouy.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1ove.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1oz1.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1r39.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1r3c.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1w7h.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/1w82.pdb', 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'224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4kip.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4kiq.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4l8m.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4loo.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4lop.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4loq.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4r3c.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4tyh.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/4zth.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5eta.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5etc.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5etf.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5eti.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5lar.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5ml5.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5mtx.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5mty.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5mz3.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5n63.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5n64.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5n65.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5n66.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5n67.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5n68.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5nzz.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5o8u.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5o8v.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5o90.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5omg.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5omh.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5tbe.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5tco.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5uoj.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5wjj.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5xyx.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/5xyy.pdb', '224c5ac9-25fc-4b30-a3b5-de67eeae6bef/6anl.pdb']\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:30,432 [MainThread  ] [INFO ]  Iterating on all clusters:\n",
      "2021-05-17 15:18:30,433 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,435 [MainThread  ] [INFO ]  ------------ Iteration #1 --------------\n",
      "2021-05-17 15:18:30,436 [MainThread  ] [INFO ]  Cluster member: 1a9u\n",
      "2021-05-17 15:18:30,507 [MainThread  ] [INFO ]  Ligand STI not found in 1a9u cluster member, skipping this cluster\n",
      "2021-05-17 15:18:30,512 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,513 [MainThread  ] [INFO ]  ------------ Iteration #2 --------------\n",
      "2021-05-17 15:18:30,514 [MainThread  ] [INFO ]  Cluster member: 1bl6\n",
      "2021-05-17 15:18:30,572 [MainThread  ] [INFO ]  Ligand STI not found in 1bl6 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:30,573 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,574 [MainThread  ] [INFO ]  ------------ Iteration #3 --------------\n",
      "2021-05-17 15:18:30,575 [MainThread  ] [INFO ]  Cluster member: 1bl7\n",
      "2021-05-17 15:18:30,618 [MainThread  ] [INFO ]  Ligand STI not found in 1bl7 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:30,619 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,620 [MainThread  ] [INFO ]  ------------ Iteration #4 --------------\n",
      "2021-05-17 15:18:30,621 [MainThread  ] [INFO ]  Cluster member: 1bmk\n",
      "2021-05-17 15:18:30,690 [MainThread  ] [INFO ]  Ligand STI not found in 1bmk cluster member, skipping this cluster\n",
      "2021-05-17 15:18:30,693 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,695 [MainThread  ] [INFO ]  ------------ Iteration #5 --------------\n",
      "2021-05-17 15:18:30,697 [MainThread  ] [INFO ]  Cluster member: 1di9\n",
      "2021-05-17 15:18:30,808 [MainThread  ] [INFO ]  Ligand STI not found in 1di9 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:30,809 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,810 [MainThread  ] [INFO ]  ------------ Iteration #6 --------------\n",
      "2021-05-17 15:18:30,811 [MainThread  ] [INFO ]  Cluster member: 1ian\n",
      "2021-05-17 15:18:30,822 [MainThread  ] [INFO ]  Ligand STI not found in 1ian cluster member, skipping this cluster\n",
      "2021-05-17 15:18:30,823 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,824 [MainThread  ] [INFO ]  ------------ Iteration #7 --------------\n",
      "2021-05-17 15:18:30,825 [MainThread  ] [INFO ]  Cluster member: 1kv1\n",
      "2021-05-17 15:18:30,886 [MainThread  ] [INFO ]  Ligand STI not found in 1kv1 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:30,887 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,888 [MainThread  ] [INFO ]  ------------ Iteration #8 --------------\n",
      "2021-05-17 15:18:30,889 [MainThread  ] [INFO ]  Cluster member: 1kv2\n",
      "2021-05-17 15:18:30,942 [MainThread  ] [INFO ]  Ligand STI not found in 1kv2 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:30,943 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,944 [MainThread  ] [INFO ]  ------------ Iteration #9 --------------\n",
      "2021-05-17 15:18:30,944 [MainThread  ] [INFO ]  Cluster member: 1lew\n",
      "2021-05-17 15:18:30,996 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 1lew\n",
      "2021-05-17 15:18:30,997 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:30,998 [MainThread  ] [INFO ]  ------------ Iteration #10 --------------\n",
      "2021-05-17 15:18:30,999 [MainThread  ] [INFO ]  Cluster member: 1lez\n",
      "2021-05-17 15:18:31,158 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 1lez\n",
      "2021-05-17 15:18:31,161 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,166 [MainThread  ] [INFO ]  ------------ Iteration #11 --------------\n",
      "2021-05-17 15:18:31,169 [MainThread  ] [INFO ]  Cluster member: 1m7q\n",
      "2021-05-17 15:18:31,286 [MainThread  ] [INFO ]  Ligand STI not found in 1m7q cluster member, skipping this cluster\n",
      "2021-05-17 15:18:31,287 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,288 [MainThread  ] [INFO ]  ------------ Iteration #12 --------------\n",
      "2021-05-17 15:18:31,288 [MainThread  ] [INFO ]  Cluster member: 1ouk\n",
      "2021-05-17 15:18:31,360 [MainThread  ] [INFO ]  Ligand STI not found in 1ouk cluster member, skipping this cluster\n",
      "2021-05-17 15:18:31,361 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,362 [MainThread  ] [INFO ]  ------------ Iteration #13 --------------\n",
      "2021-05-17 15:18:31,364 [MainThread  ] [INFO ]  Cluster member: 1ouy\n",
      "2021-05-17 15:18:31,420 [MainThread  ] [INFO ]  Ligand STI not found in 1ouy cluster member, skipping this cluster\n",
      "2021-05-17 15:18:31,422 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,423 [MainThread  ] [INFO ]  ------------ Iteration #14 --------------\n",
      "2021-05-17 15:18:31,424 [MainThread  ] [INFO ]  Cluster member: 1ove\n",
      "2021-05-17 15:18:31,525 [MainThread  ] [INFO ]  Ligand STI not found in 1ove cluster member, skipping this cluster\n",
      "2021-05-17 15:18:31,529 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,531 [MainThread  ] [INFO ]  ------------ Iteration #15 --------------\n",
      "2021-05-17 15:18:31,532 [MainThread  ] [INFO ]  Cluster member: 1oz1\n",
      "2021-05-17 15:18:31,718 [MainThread  ] [INFO ]  Ligand STI not found in 1oz1 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:31,720 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,721 [MainThread  ] [INFO ]  ------------ Iteration #16 --------------\n",
      "2021-05-17 15:18:31,722 [MainThread  ] [INFO ]  Cluster member: 1r39\n",
      "2021-05-17 15:18:31,782 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 1r39\n",
      "2021-05-17 15:18:31,783 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,783 [MainThread  ] [INFO ]  ------------ Iteration #17 --------------\n",
      "2021-05-17 15:18:31,784 [MainThread  ] [INFO ]  Cluster member: 1r3c\n",
      "2021-05-17 15:18:31,835 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 1r3c\n",
      "2021-05-17 15:18:31,836 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,837 [MainThread  ] [INFO ]  ------------ Iteration #18 --------------\n",
      "2021-05-17 15:18:31,837 [MainThread  ] [INFO ]  Cluster member: 1w7h\n",
      "2021-05-17 15:18:31,918 [MainThread  ] [INFO ]  Ligand STI not found in 1w7h cluster member, skipping this cluster\n",
      "2021-05-17 15:18:31,921 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:31,927 [MainThread  ] [INFO ]  ------------ Iteration #19 --------------\n",
      "2021-05-17 15:18:31,930 [MainThread  ] [INFO ]  Cluster member: 1w82\n",
      "2021-05-17 15:18:32,184 [MainThread  ] [INFO ]  Ligand STI not found in 1w82 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:32,184 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,185 [MainThread  ] [INFO ]  ------------ Iteration #20 --------------\n",
      "2021-05-17 15:18:32,186 [MainThread  ] [INFO ]  Cluster member: 1w83\n",
      "2021-05-17 15:18:32,244 [MainThread  ] [INFO ]  Ligand STI not found in 1w83 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:32,245 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,246 [MainThread  ] [INFO ]  ------------ Iteration #21 --------------\n",
      "2021-05-17 15:18:32,247 [MainThread  ] [INFO ]  Cluster member: 1w84\n",
      "2021-05-17 15:18:32,312 [MainThread  ] [INFO ]  Ligand STI not found in 1w84 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:32,313 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,314 [MainThread  ] [INFO ]  ------------ Iteration #22 --------------\n",
      "2021-05-17 15:18:32,315 [MainThread  ] [INFO ]  Cluster member: 1wbn\n",
      "2021-05-17 15:18:32,448 [MainThread  ] [INFO ]  Ligand STI not found in 1wbn cluster member, skipping this cluster\n",
      "2021-05-17 15:18:32,449 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,450 [MainThread  ] [INFO ]  ------------ Iteration #23 --------------\n",
      "2021-05-17 15:18:32,451 [MainThread  ] [INFO ]  Cluster member: 1wbo\n",
      "2021-05-17 15:18:32,512 [MainThread  ] [INFO ]  Ligand STI not found in 1wbo cluster member, skipping this cluster\n",
      "2021-05-17 15:18:32,513 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,514 [MainThread  ] [INFO ]  ------------ Iteration #24 --------------\n",
      "2021-05-17 15:18:32,515 [MainThread  ] [INFO ]  Cluster member: 1wbs\n",
      "2021-05-17 15:18:32,586 [MainThread  ] [INFO ]  Ligand STI not found in 1wbs cluster member, skipping this cluster\n",
      "2021-05-17 15:18:32,587 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,588 [MainThread  ] [INFO ]  ------------ Iteration #25 --------------\n",
      "2021-05-17 15:18:32,589 [MainThread  ] [INFO ]  Cluster member: 1wbt\n",
      "2021-05-17 15:18:32,674 [MainThread  ] [INFO ]  Ligand STI not found in 1wbt cluster member, skipping this cluster\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:32,675 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,676 [MainThread  ] [INFO ]  ------------ Iteration #26 --------------\n",
      "2021-05-17 15:18:32,677 [MainThread  ] [INFO ]  Cluster member: 1wbv\n",
      "2021-05-17 15:18:32,799 [MainThread  ] [INFO ]  Ligand STI not found in 1wbv cluster member, skipping this cluster\n",
      "2021-05-17 15:18:32,800 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,801 [MainThread  ] [INFO ]  ------------ Iteration #27 --------------\n",
      "2021-05-17 15:18:32,801 [MainThread  ] [INFO ]  Cluster member: 1wbw\n",
      "2021-05-17 15:18:32,850 [MainThread  ] [INFO ]  Ligand STI not found in 1wbw cluster member, skipping this cluster\n",
      "2021-05-17 15:18:32,851 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,853 [MainThread  ] [INFO ]  ------------ Iteration #28 --------------\n",
      "2021-05-17 15:18:32,854 [MainThread  ] [INFO ]  Cluster member: 1wfc\n",
      "2021-05-17 15:18:32,921 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 1wfc\n",
      "2021-05-17 15:18:32,924 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:32,925 [MainThread  ] [INFO ]  ------------ Iteration #29 --------------\n",
      "2021-05-17 15:18:32,927 [MainThread  ] [INFO ]  Cluster member: 1yqj\n",
      "2021-05-17 15:18:33,057 [MainThread  ] [INFO ]  Ligand STI not found in 1yqj cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,061 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,064 [MainThread  ] [INFO ]  ------------ Iteration #30 --------------\n",
      "2021-05-17 15:18:33,070 [MainThread  ] [INFO ]  Cluster member: 1yw2\n",
      "2021-05-17 15:18:33,215 [MainThread  ] [INFO ]  Ligand STI not found in 1yw2 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,216 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,217 [MainThread  ] [INFO ]  ------------ Iteration #31 --------------\n",
      "2021-05-17 15:18:33,217 [MainThread  ] [INFO ]  Cluster member: 1ywr\n",
      "2021-05-17 15:18:33,265 [MainThread  ] [INFO ]  Ligand STI not found in 1ywr cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,266 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,267 [MainThread  ] [INFO ]  ------------ Iteration #32 --------------\n",
      "2021-05-17 15:18:33,268 [MainThread  ] [INFO ]  Cluster member: 1zyj\n",
      "2021-05-17 15:18:33,318 [MainThread  ] [INFO ]  Ligand STI not found in 1zyj cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,319 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,320 [MainThread  ] [INFO ]  ------------ Iteration #33 --------------\n",
      "2021-05-17 15:18:33,320 [MainThread  ] [INFO ]  Cluster member: 1zz2\n",
      "2021-05-17 15:18:33,365 [MainThread  ] [INFO ]  Ligand STI not found in 1zz2 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,366 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,367 [MainThread  ] [INFO ]  ------------ Iteration #34 --------------\n",
      "2021-05-17 15:18:33,367 [MainThread  ] [INFO ]  Cluster member: 1zzl\n",
      "2021-05-17 15:18:33,411 [MainThread  ] [INFO ]  Ligand STI not found in 1zzl cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,412 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,413 [MainThread  ] [INFO ]  ------------ Iteration #35 --------------\n",
      "2021-05-17 15:18:33,413 [MainThread  ] [INFO ]  Cluster member: 2baj\n",
      "2021-05-17 15:18:33,520 [MainThread  ] [INFO ]  Ligand STI not found in 2baj cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,520 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,521 [MainThread  ] [INFO ]  ------------ Iteration #36 --------------\n",
      "2021-05-17 15:18:33,522 [MainThread  ] [INFO ]  Cluster member: 2bak\n",
      "2021-05-17 15:18:33,569 [MainThread  ] [INFO ]  Ligand STI not found in 2bak cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,570 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,571 [MainThread  ] [INFO ]  ------------ Iteration #37 --------------\n",
      "2021-05-17 15:18:33,573 [MainThread  ] [INFO ]  Cluster member: 2bal\n",
      "2021-05-17 15:18:33,623 [MainThread  ] [INFO ]  Ligand STI not found in 2bal cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,624 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,625 [MainThread  ] [INFO ]  ------------ Iteration #38 --------------\n",
      "2021-05-17 15:18:33,626 [MainThread  ] [INFO ]  Cluster member: 2baq\n",
      "2021-05-17 15:18:33,666 [MainThread  ] [INFO ]  Ligand STI not found in 2baq cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,668 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,669 [MainThread  ] [INFO ]  ------------ Iteration #39 --------------\n",
      "2021-05-17 15:18:33,669 [MainThread  ] [INFO ]  Cluster member: 2ewa\n",
      "2021-05-17 15:18:33,764 [MainThread  ] [INFO ]  Ligand STI not found in 2ewa cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,765 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,766 [MainThread  ] [INFO ]  ------------ Iteration #40 --------------\n",
      "2021-05-17 15:18:33,767 [MainThread  ] [INFO ]  Cluster member: 2fsl\n",
      "2021-05-17 15:18:33,819 [MainThread  ] [INFO ]  Ligand STI not found in 2fsl cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,820 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,820 [MainThread  ] [INFO ]  ------------ Iteration #41 --------------\n",
      "2021-05-17 15:18:33,821 [MainThread  ] [INFO ]  Cluster member: 2fsm\n",
      "2021-05-17 15:18:33,873 [MainThread  ] [INFO ]  Ligand STI not found in 2fsm cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,874 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,874 [MainThread  ] [INFO ]  ------------ Iteration #42 --------------\n",
      "2021-05-17 15:18:33,875 [MainThread  ] [INFO ]  Cluster member: 2fso\n",
      "2021-05-17 15:18:33,940 [MainThread  ] [INFO ]  Ligand STI not found in 2fso cluster member, skipping this cluster\n",
      "2021-05-17 15:18:33,940 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:33,941 [MainThread  ] [INFO ]  ------------ Iteration #43 --------------\n",
      "2021-05-17 15:18:33,942 [MainThread  ] [INFO ]  Cluster member: 2fst\n",
      "2021-05-17 15:18:34,043 [MainThread  ] [INFO ]  Ligand STI not found in 2fst cluster member, skipping this cluster\n",
      "2021-05-17 15:18:34,044 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,045 [MainThread  ] [INFO ]  ------------ Iteration #44 --------------\n",
      "2021-05-17 15:18:34,045 [MainThread  ] [INFO ]  Cluster member: 2gfs\n",
      "2021-05-17 15:18:34,099 [MainThread  ] [INFO ]  Ligand STI not found in 2gfs cluster member, skipping this cluster\n",
      "2021-05-17 15:18:34,099 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,100 [MainThread  ] [INFO ]  ------------ Iteration #45 --------------\n",
      "2021-05-17 15:18:34,101 [MainThread  ] [INFO ]  Cluster member: 2ghl\n",
      "2021-05-17 15:18:34,151 [MainThread  ] [INFO ]  Ligand STI not found in 2ghl cluster member, skipping this cluster\n",
      "2021-05-17 15:18:34,152 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,153 [MainThread  ] [INFO ]  ------------ Iteration #46 --------------\n",
      "2021-05-17 15:18:34,153 [MainThread  ] [INFO ]  Cluster member: 2ghm\n",
      "2021-05-17 15:18:34,197 [MainThread  ] [INFO ]  Ligand STI not found in 2ghm cluster member, skipping this cluster\n",
      "2021-05-17 15:18:34,198 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,198 [MainThread  ] [INFO ]  ------------ Iteration #47 --------------\n",
      "2021-05-17 15:18:34,199 [MainThread  ] [INFO ]  Cluster member: 2gtm\n",
      "2021-05-17 15:18:34,243 [MainThread  ] [INFO ]  Ligand STI not found in 2gtm cluster member, skipping this cluster\n",
      "2021-05-17 15:18:34,244 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,245 [MainThread  ] [INFO ]  ------------ Iteration #48 --------------\n",
      "2021-05-17 15:18:34,245 [MainThread  ] [INFO ]  Cluster member: 2gtn\n",
      "2021-05-17 15:18:34,353 [MainThread  ] [INFO ]  Ligand STI not found in 2gtn cluster member, skipping this cluster\n",
      "2021-05-17 15:18:34,354 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,355 [MainThread  ] [INFO ]  ------------ Iteration #49 --------------\n",
      "2021-05-17 15:18:34,357 [MainThread  ] [INFO ]  Cluster member: 2i0h\n",
      "2021-05-17 15:18:34,415 [MainThread  ] [INFO ]  Ligand STI not found in 2i0h cluster member, skipping this cluster\n",
      "2021-05-17 15:18:34,415 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,416 [MainThread  ] [INFO ]  ------------ Iteration #50 --------------\n",
      "2021-05-17 15:18:34,417 [MainThread  ] [INFO ]  Cluster member: 2lgc\n",
      "2021-05-17 15:18:34,834 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 2lgc\n",
      "2021-05-17 15:18:34,835 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,836 [MainThread  ] [INFO ]  ------------ Iteration #51 --------------\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:34,836 [MainThread  ] [INFO ]  Cluster member: 2npq\n",
      "2021-05-17 15:18:34,884 [MainThread  ] [INFO ]  Ligand STI not found in 2npq cluster member, skipping this cluster\n",
      "2021-05-17 15:18:34,885 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:34,886 [MainThread  ] [INFO ]  ------------ Iteration #52 --------------\n",
      "2021-05-17 15:18:34,887 [MainThread  ] [INFO ]  Cluster member: 2okr\n",
      "2021-05-17 15:18:35,031 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 2okr\n",
      "2021-05-17 15:18:35,032 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,033 [MainThread  ] [INFO ]  ------------ Iteration #53 --------------\n",
      "2021-05-17 15:18:35,033 [MainThread  ] [INFO ]  Cluster member: 2onl\n",
      "2021-05-17 15:18:35,213 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 2onl\n",
      "2021-05-17 15:18:35,214 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,215 [MainThread  ] [INFO ]  ------------ Iteration #54 --------------\n",
      "2021-05-17 15:18:35,215 [MainThread  ] [INFO ]  Cluster member: 2oza\n",
      "2021-05-17 15:18:35,293 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 2oza\n",
      "2021-05-17 15:18:35,294 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,295 [MainThread  ] [INFO ]  ------------ Iteration #55 --------------\n",
      "2021-05-17 15:18:35,295 [MainThread  ] [INFO ]  Cluster member: 2puu\n",
      "2021-05-17 15:18:35,343 [MainThread  ] [INFO ]  Ligand STI not found in 2puu cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,344 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,345 [MainThread  ] [INFO ]  ------------ Iteration #56 --------------\n",
      "2021-05-17 15:18:35,346 [MainThread  ] [INFO ]  Cluster member: 2qd9\n",
      "2021-05-17 15:18:35,468 [MainThread  ] [INFO ]  Ligand STI not found in 2qd9 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,469 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,470 [MainThread  ] [INFO ]  ------------ Iteration #57 --------------\n",
      "2021-05-17 15:18:35,471 [MainThread  ] [INFO ]  Cluster member: 2rg5\n",
      "2021-05-17 15:18:35,518 [MainThread  ] [INFO ]  Ligand STI not found in 2rg5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,519 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,521 [MainThread  ] [INFO ]  ------------ Iteration #58 --------------\n",
      "2021-05-17 15:18:35,522 [MainThread  ] [INFO ]  Cluster member: 2rg6\n",
      "2021-05-17 15:18:35,573 [MainThread  ] [INFO ]  Ligand STI not found in 2rg6 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,574 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,574 [MainThread  ] [INFO ]  ------------ Iteration #59 --------------\n",
      "2021-05-17 15:18:35,575 [MainThread  ] [INFO ]  Cluster member: 2y8o\n",
      "2021-05-17 15:18:35,630 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 2y8o\n",
      "2021-05-17 15:18:35,631 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,632 [MainThread  ] [INFO ]  ------------ Iteration #60 --------------\n",
      "2021-05-17 15:18:35,632 [MainThread  ] [INFO ]  Cluster member: 2yis\n",
      "2021-05-17 15:18:35,680 [MainThread  ] [INFO ]  Ligand STI not found in 2yis cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,681 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,683 [MainThread  ] [INFO ]  ------------ Iteration #61 --------------\n",
      "2021-05-17 15:18:35,683 [MainThread  ] [INFO ]  Cluster member: 2yiw\n",
      "2021-05-17 15:18:35,789 [MainThread  ] [INFO ]  Ligand STI not found in 2yiw cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,790 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,791 [MainThread  ] [INFO ]  ------------ Iteration #62 --------------\n",
      "2021-05-17 15:18:35,792 [MainThread  ] [INFO ]  Cluster member: 2yix\n",
      "2021-05-17 15:18:35,851 [MainThread  ] [INFO ]  Ligand STI not found in 2yix cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,852 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,853 [MainThread  ] [INFO ]  ------------ Iteration #63 --------------\n",
      "2021-05-17 15:18:35,853 [MainThread  ] [INFO ]  Cluster member: 2zaz\n",
      "2021-05-17 15:18:35,900 [MainThread  ] [INFO ]  Ligand STI not found in 2zaz cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,901 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,901 [MainThread  ] [INFO ]  ------------ Iteration #64 --------------\n",
      "2021-05-17 15:18:35,902 [MainThread  ] [INFO ]  Cluster member: 2zb0\n",
      "2021-05-17 15:18:35,949 [MainThread  ] [INFO ]  Ligand STI not found in 2zb0 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:35,950 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:35,951 [MainThread  ] [INFO ]  ------------ Iteration #65 --------------\n",
      "2021-05-17 15:18:35,952 [MainThread  ] [INFO ]  Cluster member: 2zb1\n",
      "2021-05-17 15:18:36,059 [MainThread  ] [INFO ]  Ligand STI not found in 2zb1 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,060 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,061 [MainThread  ] [INFO ]  ------------ Iteration #66 --------------\n",
      "2021-05-17 15:18:36,062 [MainThread  ] [INFO ]  Cluster member: 3bv2\n",
      "2021-05-17 15:18:36,102 [MainThread  ] [INFO ]  Ligand STI not found in 3bv2 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,103 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,104 [MainThread  ] [INFO ]  ------------ Iteration #67 --------------\n",
      "2021-05-17 15:18:36,104 [MainThread  ] [INFO ]  Cluster member: 3bv3\n",
      "2021-05-17 15:18:36,149 [MainThread  ] [INFO ]  Ligand STI not found in 3bv3 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,149 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,150 [MainThread  ] [INFO ]  ------------ Iteration #68 --------------\n",
      "2021-05-17 15:18:36,151 [MainThread  ] [INFO ]  Cluster member: 3bx5\n",
      "2021-05-17 15:18:36,192 [MainThread  ] [INFO ]  Ligand STI not found in 3bx5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,193 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,193 [MainThread  ] [INFO ]  ------------ Iteration #69 --------------\n",
      "2021-05-17 15:18:36,194 [MainThread  ] [INFO ]  Cluster member: 3c5u\n",
      "2021-05-17 15:18:36,291 [MainThread  ] [INFO ]  Ligand STI not found in 3c5u cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,292 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,293 [MainThread  ] [INFO ]  ------------ Iteration #70 --------------\n",
      "2021-05-17 15:18:36,294 [MainThread  ] [INFO ]  Cluster member: 3ctq\n",
      "2021-05-17 15:18:36,344 [MainThread  ] [INFO ]  Ligand STI not found in 3ctq cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,346 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,347 [MainThread  ] [INFO ]  ------------ Iteration #71 --------------\n",
      "2021-05-17 15:18:36,348 [MainThread  ] [INFO ]  Cluster member: 3d7z\n",
      "2021-05-17 15:18:36,398 [MainThread  ] [INFO ]  Ligand STI not found in 3d7z cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,399 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,400 [MainThread  ] [INFO ]  ------------ Iteration #72 --------------\n",
      "2021-05-17 15:18:36,400 [MainThread  ] [INFO ]  Cluster member: 3d83\n",
      "2021-05-17 15:18:36,449 [MainThread  ] [INFO ]  Ligand STI not found in 3d83 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,450 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,451 [MainThread  ] [INFO ]  ------------ Iteration #73 --------------\n",
      "2021-05-17 15:18:36,452 [MainThread  ] [INFO ]  Cluster member: 3ds6\n",
      "2021-05-17 15:18:36,649 [MainThread  ] [INFO ]  Ligand STI not found in 3ds6 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,650 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,651 [MainThread  ] [INFO ]  ------------ Iteration #74 --------------\n",
      "2021-05-17 15:18:36,651 [MainThread  ] [INFO ]  Cluster member: 3dt1\n",
      "2021-05-17 15:18:36,692 [MainThread  ] [INFO ]  Ligand STI not found in 3dt1 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,693 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,694 [MainThread  ] [INFO ]  ------------ Iteration #75 --------------\n",
      "2021-05-17 15:18:36,695 [MainThread  ] [INFO ]  Cluster member: 3e92\n",
      "2021-05-17 15:18:36,803 [MainThread  ] [INFO ]  Ligand STI not found in 3e92 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,804 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,805 [MainThread  ] [INFO ]  ------------ Iteration #76 --------------\n",
      "2021-05-17 15:18:36,806 [MainThread  ] [INFO ]  Cluster member: 3e93\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:36,872 [MainThread  ] [INFO ]  Ligand STI not found in 3e93 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,873 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,874 [MainThread  ] [INFO ]  ------------ Iteration #77 --------------\n",
      "2021-05-17 15:18:36,874 [MainThread  ] [INFO ]  Cluster member: 3fc1\n",
      "2021-05-17 15:18:36,919 [MainThread  ] [INFO ]  Ligand STI not found in 3fc1 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,920 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,920 [MainThread  ] [INFO ]  ------------ Iteration #78 --------------\n",
      "2021-05-17 15:18:36,921 [MainThread  ] [INFO ]  Cluster member: 3fi4\n",
      "2021-05-17 15:18:36,966 [MainThread  ] [INFO ]  Ligand STI not found in 3fi4 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:36,967 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:36,968 [MainThread  ] [INFO ]  ------------ Iteration #79 --------------\n",
      "2021-05-17 15:18:36,968 [MainThread  ] [INFO ]  Cluster member: 3fkl\n",
      "2021-05-17 15:18:37,071 [MainThread  ] [INFO ]  Ligand STI not found in 3fkl cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,072 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,073 [MainThread  ] [INFO ]  ------------ Iteration #80 --------------\n",
      "2021-05-17 15:18:37,074 [MainThread  ] [INFO ]  Cluster member: 3fkn\n",
      "2021-05-17 15:18:37,128 [MainThread  ] [INFO ]  Ligand STI not found in 3fkn cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,129 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,129 [MainThread  ] [INFO ]  ------------ Iteration #81 --------------\n",
      "2021-05-17 15:18:37,131 [MainThread  ] [INFO ]  Cluster member: 3fko\n",
      "2021-05-17 15:18:37,182 [MainThread  ] [INFO ]  Ligand STI not found in 3fko cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,183 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,184 [MainThread  ] [INFO ]  ------------ Iteration #82 --------------\n",
      "2021-05-17 15:18:37,184 [MainThread  ] [INFO ]  Cluster member: 3fl4\n",
      "2021-05-17 15:18:37,235 [MainThread  ] [INFO ]  Ligand STI not found in 3fl4 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,236 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,236 [MainThread  ] [INFO ]  ------------ Iteration #83 --------------\n",
      "2021-05-17 15:18:37,237 [MainThread  ] [INFO ]  Cluster member: 3fln\n",
      "2021-05-17 15:18:37,336 [MainThread  ] [INFO ]  Ligand STI not found in 3fln cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,337 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,337 [MainThread  ] [INFO ]  ------------ Iteration #84 --------------\n",
      "2021-05-17 15:18:37,338 [MainThread  ] [INFO ]  Cluster member: 3flq\n",
      "2021-05-17 15:18:37,390 [MainThread  ] [INFO ]  Ligand STI not found in 3flq cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,391 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,391 [MainThread  ] [INFO ]  ------------ Iteration #85 --------------\n",
      "2021-05-17 15:18:37,392 [MainThread  ] [INFO ]  Cluster member: 3fls\n",
      "2021-05-17 15:18:37,434 [MainThread  ] [INFO ]  Ligand STI not found in 3fls cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,435 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,435 [MainThread  ] [INFO ]  ------------ Iteration #86 --------------\n",
      "2021-05-17 15:18:37,436 [MainThread  ] [INFO ]  Cluster member: 3flw\n",
      "2021-05-17 15:18:37,481 [MainThread  ] [INFO ]  Ligand STI not found in 3flw cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,482 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,482 [MainThread  ] [INFO ]  ------------ Iteration #87 --------------\n",
      "2021-05-17 15:18:37,483 [MainThread  ] [INFO ]  Cluster member: 3fly\n",
      "2021-05-17 15:18:37,528 [MainThread  ] [INFO ]  Ligand STI not found in 3fly cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,528 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,529 [MainThread  ] [INFO ]  ------------ Iteration #88 --------------\n",
      "2021-05-17 15:18:37,530 [MainThread  ] [INFO ]  Cluster member: 3flz\n",
      "2021-05-17 15:18:37,638 [MainThread  ] [INFO ]  Ligand STI not found in 3flz cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,639 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,639 [MainThread  ] [INFO ]  ------------ Iteration #89 --------------\n",
      "2021-05-17 15:18:37,640 [MainThread  ] [INFO ]  Cluster member: 3fmh\n",
      "2021-05-17 15:18:37,683 [MainThread  ] [INFO ]  Ligand STI not found in 3fmh cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,684 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,685 [MainThread  ] [INFO ]  ------------ Iteration #90 --------------\n",
      "2021-05-17 15:18:37,685 [MainThread  ] [INFO ]  Cluster member: 3fmj\n",
      "2021-05-17 15:18:37,732 [MainThread  ] [INFO ]  Ligand STI not found in 3fmj cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,733 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,733 [MainThread  ] [INFO ]  ------------ Iteration #91 --------------\n",
      "2021-05-17 15:18:37,734 [MainThread  ] [INFO ]  Cluster member: 3fmk\n",
      "2021-05-17 15:18:37,781 [MainThread  ] [INFO ]  Ligand STI not found in 3fmk cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,782 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,784 [MainThread  ] [INFO ]  ------------ Iteration #92 --------------\n",
      "2021-05-17 15:18:37,785 [MainThread  ] [INFO ]  Cluster member: 3fml\n",
      "2021-05-17 15:18:37,883 [MainThread  ] [INFO ]  Ligand STI not found in 3fml cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,884 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,884 [MainThread  ] [INFO ]  ------------ Iteration #93 --------------\n",
      "2021-05-17 15:18:37,885 [MainThread  ] [INFO ]  Cluster member: 3fmm\n",
      "2021-05-17 15:18:37,929 [MainThread  ] [INFO ]  Ligand STI not found in 3fmm cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,930 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,931 [MainThread  ] [INFO ]  ------------ Iteration #94 --------------\n",
      "2021-05-17 15:18:37,931 [MainThread  ] [INFO ]  Cluster member: 3fmn\n",
      "2021-05-17 15:18:37,988 [MainThread  ] [INFO ]  Ligand STI not found in 3fmn cluster member, skipping this cluster\n",
      "2021-05-17 15:18:37,989 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:37,989 [MainThread  ] [INFO ]  ------------ Iteration #95 --------------\n",
      "2021-05-17 15:18:37,990 [MainThread  ] [INFO ]  Cluster member: 3fsf\n",
      "2021-05-17 15:18:38,031 [MainThread  ] [INFO ]  Ligand STI not found in 3fsf cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,032 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,032 [MainThread  ] [INFO ]  ------------ Iteration #96 --------------\n",
      "2021-05-17 15:18:38,033 [MainThread  ] [INFO ]  Cluster member: 3fsk\n",
      "2021-05-17 15:18:38,129 [MainThread  ] [INFO ]  Ligand STI not found in 3fsk cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,130 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,131 [MainThread  ] [INFO ]  ------------ Iteration #97 --------------\n",
      "2021-05-17 15:18:38,131 [MainThread  ] [INFO ]  Cluster member: 3gc7\n",
      "2021-05-17 15:18:38,186 [MainThread  ] [INFO ]  Ligand STI not found in 3gc7 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,186 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,187 [MainThread  ] [INFO ]  ------------ Iteration #98 --------------\n",
      "2021-05-17 15:18:38,187 [MainThread  ] [INFO ]  Cluster member: 3gcp\n",
      "2021-05-17 15:18:38,231 [MainThread  ] [INFO ]  Ligand STI not found in 3gcp cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,232 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,233 [MainThread  ] [INFO ]  ------------ Iteration #99 --------------\n",
      "2021-05-17 15:18:38,233 [MainThread  ] [INFO ]  Cluster member: 3gcq\n",
      "2021-05-17 15:18:38,277 [MainThread  ] [INFO ]  Ligand STI not found in 3gcq cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,278 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,278 [MainThread  ] [INFO ]  ------------ Iteration #100 --------------\n",
      "2021-05-17 15:18:38,279 [MainThread  ] [INFO ]  Cluster member: 3gcs\n",
      "2021-05-17 15:18:38,383 [MainThread  ] [INFO ]  Ligand STI not found in 3gcs cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,384 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,385 [MainThread  ] [INFO ]  ------------ Iteration #101 --------------\n",
      "2021-05-17 15:18:38,386 [MainThread  ] [INFO ]  Cluster member: 3gcu\n",
      "2021-05-17 15:18:38,469 [MainThread  ] [INFO ]  Ligand STI not found in 3gcu cluster member, skipping this cluster\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:38,469 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,470 [MainThread  ] [INFO ]  ------------ Iteration #102 --------------\n",
      "2021-05-17 15:18:38,471 [MainThread  ] [INFO ]  Cluster member: 3gcv\n",
      "2021-05-17 15:18:38,512 [MainThread  ] [INFO ]  Ligand STI not found in 3gcv cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,513 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,513 [MainThread  ] [INFO ]  ------------ Iteration #103 --------------\n",
      "2021-05-17 15:18:38,514 [MainThread  ] [INFO ]  Cluster member: 3gfe\n",
      "2021-05-17 15:18:38,608 [MainThread  ] [INFO ]  Ligand STI not found in 3gfe cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,609 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,617 [MainThread  ] [INFO ]  ------------ Iteration #104 --------------\n",
      "2021-05-17 15:18:38,618 [MainThread  ] [INFO ]  Cluster member: 3gi3\n",
      "2021-05-17 15:18:38,672 [MainThread  ] [INFO ]  Ligand STI not found in 3gi3 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,673 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,673 [MainThread  ] [INFO ]  ------------ Iteration #105 --------------\n",
      "2021-05-17 15:18:38,674 [MainThread  ] [INFO ]  Cluster member: 3ha8\n",
      "2021-05-17 15:18:38,722 [MainThread  ] [INFO ]  Ligand STI not found in 3ha8 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,723 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,724 [MainThread  ] [INFO ]  ------------ Iteration #106 --------------\n",
      "2021-05-17 15:18:38,725 [MainThread  ] [INFO ]  Cluster member: 3hec\n",
      "2021-05-17 15:18:38,769 [MainThread  ] [INFO ]  Ligand found: STI  (37 atoms)\n",
      "2021-05-17 15:18:38,770 [MainThread  ] [INFO ]  Member accepted. Valid ligand found: STI (37 atoms)\n",
      "2021-05-17 15:18:38,825 [MainThread  ] [INFO ]  Matching residues to input PDB structure. Alignment is:\n",
      "RPTFYRQELNKTIWEVPERYQNLSPVGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPP\n",
      "2021-05-17 15:18:38,826 [MainThread  ] [INFO ]  Sequence identity (%): 100.0\n",
      "2021-05-17 15:18:38,826 [MainThread  ] [INFO ]  Gap less identity (%): 100.0\n",
      "2021-05-17 15:18:38,844 [MainThread  ] [INFO ]  Superimposing 329 aligned protein residues\n",
      "2021-05-17 15:18:38,863 [MainThread  ] [INFO ]  RMSD: 1.3543451279629504e-14\n",
      "2021-05-17 15:18:38,866 [MainThread  ] [INFO ]  Saving transformed ligand coordinates\n",
      "2021-05-17 15:18:38,867 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,868 [MainThread  ] [INFO ]  ------------ Iteration #107 --------------\n",
      "2021-05-17 15:18:38,871 [MainThread  ] [INFO ]  Cluster member: 3heg\n",
      "2021-05-17 15:18:38,920 [MainThread  ] [INFO ]  Ligand STI not found in 3heg cluster member, skipping this cluster\n",
      "2021-05-17 15:18:38,921 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:38,922 [MainThread  ] [INFO ]  ------------ Iteration #108 --------------\n",
      "2021-05-17 15:18:38,923 [MainThread  ] [INFO ]  Cluster member: 3hl7\n",
      "2021-05-17 15:18:39,029 [MainThread  ] [INFO ]  Ligand STI not found in 3hl7 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,030 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,031 [MainThread  ] [INFO ]  ------------ Iteration #109 --------------\n",
      "2021-05-17 15:18:39,032 [MainThread  ] [INFO ]  Cluster member: 3hll\n",
      "2021-05-17 15:18:39,075 [MainThread  ] [INFO ]  Ligand STI not found in 3hll cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,076 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,077 [MainThread  ] [INFO ]  ------------ Iteration #110 --------------\n",
      "2021-05-17 15:18:39,077 [MainThread  ] [INFO ]  Cluster member: 3hp2\n",
      "2021-05-17 15:18:39,129 [MainThread  ] [INFO ]  Ligand STI not found in 3hp2 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,130 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,130 [MainThread  ] [INFO ]  ------------ Iteration #111 --------------\n",
      "2021-05-17 15:18:39,131 [MainThread  ] [INFO ]  Cluster member: 3hp5\n",
      "2021-05-17 15:18:39,175 [MainThread  ] [INFO ]  Ligand STI not found in 3hp5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,176 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,176 [MainThread  ] [INFO ]  ------------ Iteration #112 --------------\n",
      "2021-05-17 15:18:39,177 [MainThread  ] [INFO ]  Cluster member: 3hrb\n",
      "2021-05-17 15:18:39,283 [MainThread  ] [INFO ]  Ligand STI not found in 3hrb cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,284 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,285 [MainThread  ] [INFO ]  ------------ Iteration #113 --------------\n",
      "2021-05-17 15:18:39,285 [MainThread  ] [INFO ]  Cluster member: 3hub\n",
      "2021-05-17 15:18:39,330 [MainThread  ] [INFO ]  Ligand STI not found in 3hub cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,331 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,332 [MainThread  ] [INFO ]  ------------ Iteration #114 --------------\n",
      "2021-05-17 15:18:39,332 [MainThread  ] [INFO ]  Cluster member: 3huc\n",
      "2021-05-17 15:18:39,377 [MainThread  ] [INFO ]  Ligand STI not found in 3huc cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,378 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,379 [MainThread  ] [INFO ]  ------------ Iteration #115 --------------\n",
      "2021-05-17 15:18:39,379 [MainThread  ] [INFO ]  Cluster member: 3hv3\n",
      "2021-05-17 15:18:39,430 [MainThread  ] [INFO ]  Ligand STI not found in 3hv3 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,431 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,432 [MainThread  ] [INFO ]  ------------ Iteration #116 --------------\n",
      "2021-05-17 15:18:39,433 [MainThread  ] [INFO ]  Cluster member: 3hv4\n",
      "2021-05-17 15:18:39,567 [MainThread  ] [INFO ]  Ligand STI not found in 3hv4 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,568 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,568 [MainThread  ] [INFO ]  ------------ Iteration #117 --------------\n",
      "2021-05-17 15:18:39,569 [MainThread  ] [INFO ]  Cluster member: 3hv5\n",
      "2021-05-17 15:18:39,647 [MainThread  ] [INFO ]  Ligand STI not found in 3hv5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,648 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,648 [MainThread  ] [INFO ]  ------------ Iteration #118 --------------\n",
      "2021-05-17 15:18:39,649 [MainThread  ] [INFO ]  Cluster member: 3hv6\n",
      "2021-05-17 15:18:39,690 [MainThread  ] [INFO ]  Ligand STI not found in 3hv6 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,691 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,691 [MainThread  ] [INFO ]  ------------ Iteration #119 --------------\n",
      "2021-05-17 15:18:39,692 [MainThread  ] [INFO ]  Cluster member: 3hv7\n",
      "2021-05-17 15:18:39,794 [MainThread  ] [INFO ]  Ligand STI not found in 3hv7 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,795 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,796 [MainThread  ] [INFO ]  ------------ Iteration #120 --------------\n",
      "2021-05-17 15:18:39,797 [MainThread  ] [INFO ]  Cluster member: 3hvc\n",
      "2021-05-17 15:18:39,851 [MainThread  ] [INFO ]  Ligand STI not found in 3hvc cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,852 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,852 [MainThread  ] [INFO ]  ------------ Iteration #121 --------------\n",
      "2021-05-17 15:18:39,853 [MainThread  ] [INFO ]  Cluster member: 3iph\n",
      "2021-05-17 15:18:39,906 [MainThread  ] [INFO ]  Ligand STI not found in 3iph cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,907 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,908 [MainThread  ] [INFO ]  ------------ Iteration #122 --------------\n",
      "2021-05-17 15:18:39,909 [MainThread  ] [INFO ]  Cluster member: 3itz\n",
      "2021-05-17 15:18:39,955 [MainThread  ] [INFO ]  Ligand STI not found in 3itz cluster member, skipping this cluster\n",
      "2021-05-17 15:18:39,956 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:39,956 [MainThread  ] [INFO ]  ------------ Iteration #123 --------------\n",
      "2021-05-17 15:18:39,957 [MainThread  ] [INFO ]  Cluster member: 3iw5\n",
      "2021-05-17 15:18:40,001 [MainThread  ] [INFO ]  Ligand STI not found in 3iw5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,002 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,002 [MainThread  ] [INFO ]  ------------ Iteration #124 --------------\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:40,003 [MainThread  ] [INFO ]  Cluster member: 3iw6\n",
      "2021-05-17 15:18:40,113 [MainThread  ] [INFO ]  Ligand STI not found in 3iw6 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,114 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,115 [MainThread  ] [INFO ]  ------------ Iteration #125 --------------\n",
      "2021-05-17 15:18:40,115 [MainThread  ] [INFO ]  Cluster member: 3iw7\n",
      "2021-05-17 15:18:40,156 [MainThread  ] [INFO ]  Ligand STI not found in 3iw7 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,157 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,157 [MainThread  ] [INFO ]  ------------ Iteration #126 --------------\n",
      "2021-05-17 15:18:40,158 [MainThread  ] [INFO ]  Cluster member: 3iw8\n",
      "2021-05-17 15:18:40,205 [MainThread  ] [INFO ]  Ligand STI not found in 3iw8 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,206 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,206 [MainThread  ] [INFO ]  ------------ Iteration #127 --------------\n",
      "2021-05-17 15:18:40,207 [MainThread  ] [INFO ]  Cluster member: 3k3i\n",
      "2021-05-17 15:18:40,255 [MainThread  ] [INFO ]  Ligand STI not found in 3k3i cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,256 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,257 [MainThread  ] [INFO ]  ------------ Iteration #128 --------------\n",
      "2021-05-17 15:18:40,258 [MainThread  ] [INFO ]  Cluster member: 3k3j\n",
      "2021-05-17 15:18:40,359 [MainThread  ] [INFO ]  Ligand STI not found in 3k3j cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,360 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,361 [MainThread  ] [INFO ]  ------------ Iteration #129 --------------\n",
      "2021-05-17 15:18:40,361 [MainThread  ] [INFO ]  Cluster member: 3kf7\n",
      "2021-05-17 15:18:40,416 [MainThread  ] [INFO ]  Ligand STI not found in 3kf7 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,417 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,418 [MainThread  ] [INFO ]  ------------ Iteration #130 --------------\n",
      "2021-05-17 15:18:40,418 [MainThread  ] [INFO ]  Cluster member: 3kq7\n",
      "2021-05-17 15:18:40,473 [MainThread  ] [INFO ]  Ligand STI not found in 3kq7 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,474 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,475 [MainThread  ] [INFO ]  ------------ Iteration #131 --------------\n",
      "2021-05-17 15:18:40,475 [MainThread  ] [INFO ]  Cluster member: 3l8s\n",
      "2021-05-17 15:18:40,523 [MainThread  ] [INFO ]  Ligand STI not found in 3l8s cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,524 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,525 [MainThread  ] [INFO ]  ------------ Iteration #132 --------------\n",
      "2021-05-17 15:18:40,526 [MainThread  ] [INFO ]  Cluster member: 3l8x\n",
      "2021-05-17 15:18:40,623 [MainThread  ] [INFO ]  Ligand STI not found in 3l8x cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,624 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,624 [MainThread  ] [INFO ]  ------------ Iteration #133 --------------\n",
      "2021-05-17 15:18:40,625 [MainThread  ] [INFO ]  Cluster member: 3lfa\n",
      "2021-05-17 15:18:40,674 [MainThread  ] [INFO ]  Ligand STI not found in 3lfa cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,675 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,676 [MainThread  ] [INFO ]  ------------ Iteration #134 --------------\n",
      "2021-05-17 15:18:40,677 [MainThread  ] [INFO ]  Cluster member: 3lfb\n",
      "2021-05-17 15:18:40,731 [MainThread  ] [INFO ]  Ligand STI not found in 3lfb cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,732 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,732 [MainThread  ] [INFO ]  ------------ Iteration #135 --------------\n",
      "2021-05-17 15:18:40,733 [MainThread  ] [INFO ]  Cluster member: 3lfc\n",
      "2021-05-17 15:18:40,779 [MainThread  ] [INFO ]  Ligand STI not found in 3lfc cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,780 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,781 [MainThread  ] [INFO ]  ------------ Iteration #136 --------------\n",
      "2021-05-17 15:18:40,783 [MainThread  ] [INFO ]  Cluster member: 3lfd\n",
      "2021-05-17 15:18:40,826 [MainThread  ] [INFO ]  Ligand STI not found in 3lfd cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,827 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,828 [MainThread  ] [INFO ]  ------------ Iteration #137 --------------\n",
      "2021-05-17 15:18:40,828 [MainThread  ] [INFO ]  Cluster member: 3lfe\n",
      "2021-05-17 15:18:40,930 [MainThread  ] [INFO ]  Ligand STI not found in 3lfe cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,931 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,932 [MainThread  ] [INFO ]  ------------ Iteration #138 --------------\n",
      "2021-05-17 15:18:40,932 [MainThread  ] [INFO ]  Cluster member: 3lff\n",
      "2021-05-17 15:18:40,989 [MainThread  ] [INFO ]  Ligand STI not found in 3lff cluster member, skipping this cluster\n",
      "2021-05-17 15:18:40,990 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:40,991 [MainThread  ] [INFO ]  ------------ Iteration #139 --------------\n",
      "2021-05-17 15:18:40,991 [MainThread  ] [INFO ]  Cluster member: 3lhj\n",
      "2021-05-17 15:18:41,037 [MainThread  ] [INFO ]  Ligand STI not found in 3lhj cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,038 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,039 [MainThread  ] [INFO ]  ------------ Iteration #140 --------------\n",
      "2021-05-17 15:18:41,040 [MainThread  ] [INFO ]  Cluster member: 3mgy\n",
      "2021-05-17 15:18:41,084 [MainThread  ] [INFO ]  Ligand STI not found in 3mgy cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,085 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,085 [MainThread  ] [INFO ]  ------------ Iteration #141 --------------\n",
      "2021-05-17 15:18:41,086 [MainThread  ] [INFO ]  Cluster member: 3mh0\n",
      "2021-05-17 15:18:41,130 [MainThread  ] [INFO ]  Ligand STI not found in 3mh0 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,131 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,131 [MainThread  ] [INFO ]  ------------ Iteration #142 --------------\n",
      "2021-05-17 15:18:41,132 [MainThread  ] [INFO ]  Cluster member: 3mh1\n",
      "2021-05-17 15:18:41,236 [MainThread  ] [INFO ]  Ligand STI not found in 3mh1 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,237 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,237 [MainThread  ] [INFO ]  ------------ Iteration #143 --------------\n",
      "2021-05-17 15:18:41,238 [MainThread  ] [INFO ]  Cluster member: 3mh2\n",
      "2021-05-17 15:18:41,279 [MainThread  ] [INFO ]  Ligand STI not found in 3mh2 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,280 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,281 [MainThread  ] [INFO ]  ------------ Iteration #144 --------------\n",
      "2021-05-17 15:18:41,281 [MainThread  ] [INFO ]  Cluster member: 3mh3\n",
      "2021-05-17 15:18:41,336 [MainThread  ] [INFO ]  Ligand STI not found in 3mh3 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,337 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,337 [MainThread  ] [INFO ]  ------------ Iteration #145 --------------\n",
      "2021-05-17 15:18:41,338 [MainThread  ] [INFO ]  Cluster member: 3mpa\n",
      "2021-05-17 15:18:41,388 [MainThread  ] [INFO ]  Ligand STI not found in 3mpa cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,389 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,389 [MainThread  ] [INFO ]  ------------ Iteration #146 --------------\n",
      "2021-05-17 15:18:41,390 [MainThread  ] [INFO ]  Cluster member: 3mpt\n",
      "2021-05-17 15:18:41,490 [MainThread  ] [INFO ]  Ligand STI not found in 3mpt cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,491 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,492 [MainThread  ] [INFO ]  ------------ Iteration #147 --------------\n",
      "2021-05-17 15:18:41,492 [MainThread  ] [INFO ]  Cluster member: 3mvl\n",
      "2021-05-17 15:18:41,573 [MainThread  ] [INFO ]  Ligand STI not found in 3mvl cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,574 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,575 [MainThread  ] [INFO ]  ------------ Iteration #148 --------------\n",
      "2021-05-17 15:18:41,575 [MainThread  ] [INFO ]  Cluster member: 3mvm\n",
      "2021-05-17 15:18:41,661 [MainThread  ] [INFO ]  Ligand STI not found in 3mvm cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,662 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,663 [MainThread  ] [INFO ]  ------------ Iteration #149 --------------\n",
      "2021-05-17 15:18:41,663 [MainThread  ] [INFO ]  Cluster member: 3mw1\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:41,774 [MainThread  ] [INFO ]  Ligand STI not found in 3mw1 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,775 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,776 [MainThread  ] [INFO ]  ------------ Iteration #150 --------------\n",
      "2021-05-17 15:18:41,776 [MainThread  ] [INFO ]  Cluster member: 3new\n",
      "2021-05-17 15:18:41,821 [MainThread  ] [INFO ]  Ligand STI not found in 3new cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,821 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,822 [MainThread  ] [INFO ]  ------------ Iteration #151 --------------\n",
      "2021-05-17 15:18:41,823 [MainThread  ] [INFO ]  Cluster member: 3nnu\n",
      "2021-05-17 15:18:41,870 [MainThread  ] [INFO ]  Ligand STI not found in 3nnu cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,870 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,871 [MainThread  ] [INFO ]  ------------ Iteration #152 --------------\n",
      "2021-05-17 15:18:41,872 [MainThread  ] [INFO ]  Cluster member: 3nnv\n",
      "2021-05-17 15:18:41,921 [MainThread  ] [INFO ]  Ligand STI not found in 3nnv cluster member, skipping this cluster\n",
      "2021-05-17 15:18:41,922 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:41,923 [MainThread  ] [INFO ]  ------------ Iteration #153 --------------\n",
      "2021-05-17 15:18:41,923 [MainThread  ] [INFO ]  Cluster member: 3nnw\n",
      "2021-05-17 15:18:42,046 [MainThread  ] [INFO ]  Ligand STI not found in 3nnw cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,047 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,047 [MainThread  ] [INFO ]  ------------ Iteration #154 --------------\n",
      "2021-05-17 15:18:42,048 [MainThread  ] [INFO ]  Cluster member: 3nnx\n",
      "2021-05-17 15:18:42,104 [MainThread  ] [INFO ]  Ligand STI not found in 3nnx cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,105 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,106 [MainThread  ] [INFO ]  ------------ Iteration #155 --------------\n",
      "2021-05-17 15:18:42,106 [MainThread  ] [INFO ]  Cluster member: 3nww\n",
      "2021-05-17 15:18:42,155 [MainThread  ] [INFO ]  Ligand STI not found in 3nww cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,156 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,157 [MainThread  ] [INFO ]  ------------ Iteration #156 --------------\n",
      "2021-05-17 15:18:42,157 [MainThread  ] [INFO ]  Cluster member: 3o8p\n",
      "2021-05-17 15:18:42,207 [MainThread  ] [INFO ]  Ligand STI not found in 3o8p cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,208 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,209 [MainThread  ] [INFO ]  ------------ Iteration #157 --------------\n",
      "2021-05-17 15:18:42,209 [MainThread  ] [INFO ]  Cluster member: 3o8t\n",
      "2021-05-17 15:18:42,309 [MainThread  ] [INFO ]  Ligand STI not found in 3o8t cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,310 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,311 [MainThread  ] [INFO ]  ------------ Iteration #158 --------------\n",
      "2021-05-17 15:18:42,312 [MainThread  ] [INFO ]  Cluster member: 3o8u\n",
      "2021-05-17 15:18:42,361 [MainThread  ] [INFO ]  Ligand STI not found in 3o8u cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,362 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,363 [MainThread  ] [INFO ]  ------------ Iteration #159 --------------\n",
      "2021-05-17 15:18:42,363 [MainThread  ] [INFO ]  Cluster member: 3obg\n",
      "2021-05-17 15:18:42,413 [MainThread  ] [INFO ]  Ligand STI not found in 3obg cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,414 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,415 [MainThread  ] [INFO ]  ------------ Iteration #160 --------------\n",
      "2021-05-17 15:18:42,416 [MainThread  ] [INFO ]  Cluster member: 3obj\n",
      "2021-05-17 15:18:42,473 [MainThread  ] [INFO ]  Ligand STI not found in 3obj cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,474 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,474 [MainThread  ] [INFO ]  ------------ Iteration #161 --------------\n",
      "2021-05-17 15:18:42,476 [MainThread  ] [INFO ]  Cluster member: 3oc1\n",
      "2021-05-17 15:18:42,520 [MainThread  ] [INFO ]  Ligand STI not found in 3oc1 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,521 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,522 [MainThread  ] [INFO ]  ------------ Iteration #162 --------------\n",
      "2021-05-17 15:18:42,523 [MainThread  ] [INFO ]  Cluster member: 3ocg\n",
      "2021-05-17 15:18:42,630 [MainThread  ] [INFO ]  Ligand STI not found in 3ocg cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,630 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,631 [MainThread  ] [INFO ]  ------------ Iteration #163 --------------\n",
      "2021-05-17 15:18:42,632 [MainThread  ] [INFO ]  Cluster member: 3od6\n",
      "2021-05-17 15:18:42,685 [MainThread  ] [INFO ]  Ligand STI not found in 3od6 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,686 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,686 [MainThread  ] [INFO ]  ------------ Iteration #164 --------------\n",
      "2021-05-17 15:18:42,687 [MainThread  ] [INFO ]  Cluster member: 3ody\n",
      "2021-05-17 15:18:42,728 [MainThread  ] [INFO ]  Ligand STI not found in 3ody cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,729 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,729 [MainThread  ] [INFO ]  ------------ Iteration #165 --------------\n",
      "2021-05-17 15:18:42,730 [MainThread  ] [INFO ]  Cluster member: 3odz\n",
      "2021-05-17 15:18:42,792 [MainThread  ] [INFO ]  Ligand STI not found in 3odz cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,793 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,793 [MainThread  ] [INFO ]  ------------ Iteration #166 --------------\n",
      "2021-05-17 15:18:42,794 [MainThread  ] [INFO ]  Cluster member: 3oef\n",
      "2021-05-17 15:18:42,844 [MainThread  ] [INFO ]  Ligand STI not found in 3oef cluster member, skipping this cluster\n",
      "2021-05-17 15:18:42,845 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,845 [MainThread  ] [INFO ]  ------------ Iteration #167 --------------\n",
      "2021-05-17 15:18:42,846 [MainThread  ] [INFO ]  Cluster member: 3p4k\n",
      "2021-05-17 15:18:42,958 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 3p4k\n",
      "2021-05-17 15:18:42,959 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:42,960 [MainThread  ] [INFO ]  ------------ Iteration #168 --------------\n",
      "2021-05-17 15:18:42,960 [MainThread  ] [INFO ]  Cluster member: 3p5k\n",
      "2021-05-17 15:18:43,006 [MainThread  ] [INFO ]  Ligand STI not found in 3p5k cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,007 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,007 [MainThread  ] [INFO ]  ------------ Iteration #169 --------------\n",
      "2021-05-17 15:18:43,008 [MainThread  ] [INFO ]  Cluster member: 3p78\n",
      "2021-05-17 15:18:43,050 [MainThread  ] [INFO ]  Ligand STI not found in 3p78 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,051 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,052 [MainThread  ] [INFO ]  ------------ Iteration #170 --------------\n",
      "2021-05-17 15:18:43,053 [MainThread  ] [INFO ]  Cluster member: 3p79\n",
      "2021-05-17 15:18:43,098 [MainThread  ] [INFO ]  Ligand STI not found in 3p79 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,098 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,099 [MainThread  ] [INFO ]  ------------ Iteration #171 --------------\n",
      "2021-05-17 15:18:43,100 [MainThread  ] [INFO ]  Cluster member: 3p7a\n",
      "2021-05-17 15:18:43,195 [MainThread  ] [INFO ]  Ligand STI not found in 3p7a cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,196 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,197 [MainThread  ] [INFO ]  ------------ Iteration #172 --------------\n",
      "2021-05-17 15:18:43,199 [MainThread  ] [INFO ]  Cluster member: 3p7b\n",
      "2021-05-17 15:18:43,261 [MainThread  ] [INFO ]  Ligand STI not found in 3p7b cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,262 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,263 [MainThread  ] [INFO ]  ------------ Iteration #173 --------------\n",
      "2021-05-17 15:18:43,263 [MainThread  ] [INFO ]  Cluster member: 3p7c\n",
      "2021-05-17 15:18:43,306 [MainThread  ] [INFO ]  Ligand STI not found in 3p7c cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,307 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,307 [MainThread  ] [INFO ]  ------------ Iteration #174 --------------\n",
      "2021-05-17 15:18:43,308 [MainThread  ] [INFO ]  Cluster member: 3pg3\n",
      "2021-05-17 15:18:43,353 [MainThread  ] [INFO ]  Ligand STI not found in 3pg3 cluster member, skipping this cluster\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:43,354 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,354 [MainThread  ] [INFO ]  ------------ Iteration #175 --------------\n",
      "2021-05-17 15:18:43,355 [MainThread  ] [INFO ]  Cluster member: 3py3\n",
      "2021-05-17 15:18:43,403 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 3py3\n",
      "2021-05-17 15:18:43,404 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,405 [MainThread  ] [INFO ]  ------------ Iteration #176 --------------\n",
      "2021-05-17 15:18:43,406 [MainThread  ] [INFO ]  Cluster member: 3qud\n",
      "2021-05-17 15:18:43,513 [MainThread  ] [INFO ]  Ligand STI not found in 3qud cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,514 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,514 [MainThread  ] [INFO ]  ------------ Iteration #177 --------------\n",
      "2021-05-17 15:18:43,515 [MainThread  ] [INFO ]  Cluster member: 3que\n",
      "2021-05-17 15:18:43,569 [MainThread  ] [INFO ]  Ligand STI not found in 3que cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,569 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,570 [MainThread  ] [INFO ]  ------------ Iteration #178 --------------\n",
      "2021-05-17 15:18:43,571 [MainThread  ] [INFO ]  Cluster member: 3rin\n",
      "2021-05-17 15:18:43,617 [MainThread  ] [INFO ]  Ligand STI not found in 3rin cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,617 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,618 [MainThread  ] [INFO ]  ------------ Iteration #179 --------------\n",
      "2021-05-17 15:18:43,619 [MainThread  ] [INFO ]  Cluster member: 3roc\n",
      "2021-05-17 15:18:43,670 [MainThread  ] [INFO ]  Ligand STI not found in 3roc cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,671 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,672 [MainThread  ] [INFO ]  ------------ Iteration #180 --------------\n",
      "2021-05-17 15:18:43,672 [MainThread  ] [INFO ]  Cluster member: 3s3i\n",
      "2021-05-17 15:18:43,774 [MainThread  ] [INFO ]  Ligand STI not found in 3s3i cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,775 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,776 [MainThread  ] [INFO ]  ------------ Iteration #181 --------------\n",
      "2021-05-17 15:18:43,777 [MainThread  ] [INFO ]  Cluster member: 3s4q\n",
      "2021-05-17 15:18:43,819 [MainThread  ] [INFO ]  Ligand STI not found in 3s4q cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,820 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,821 [MainThread  ] [INFO ]  ------------ Iteration #182 --------------\n",
      "2021-05-17 15:18:43,821 [MainThread  ] [INFO ]  Cluster member: 3tg1\n",
      "2021-05-17 15:18:43,871 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 3tg1\n",
      "2021-05-17 15:18:43,872 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,873 [MainThread  ] [INFO ]  ------------ Iteration #183 --------------\n",
      "2021-05-17 15:18:43,873 [MainThread  ] [INFO ]  Cluster member: 3u8w\n",
      "2021-05-17 15:18:43,914 [MainThread  ] [INFO ]  Ligand STI not found in 3u8w cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,915 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,916 [MainThread  ] [INFO ]  ------------ Iteration #184 --------------\n",
      "2021-05-17 15:18:43,916 [MainThread  ] [INFO ]  Cluster member: 3uvp\n",
      "2021-05-17 15:18:43,963 [MainThread  ] [INFO ]  Ligand STI not found in 3uvp cluster member, skipping this cluster\n",
      "2021-05-17 15:18:43,964 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:43,965 [MainThread  ] [INFO ]  ------------ Iteration #185 --------------\n",
      "2021-05-17 15:18:43,965 [MainThread  ] [INFO ]  Cluster member: 3uvq\n",
      "2021-05-17 15:18:44,080 [MainThread  ] [INFO ]  Ligand STI not found in 3uvq cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,081 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,082 [MainThread  ] [INFO ]  ------------ Iteration #186 --------------\n",
      "2021-05-17 15:18:44,082 [MainThread  ] [INFO ]  Cluster member: 3uvr\n",
      "2021-05-17 15:18:44,131 [MainThread  ] [INFO ]  Ligand STI not found in 3uvr cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,132 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,133 [MainThread  ] [INFO ]  ------------ Iteration #187 --------------\n",
      "2021-05-17 15:18:44,135 [MainThread  ] [INFO ]  Cluster member: 3zs5\n",
      "2021-05-17 15:18:44,186 [MainThread  ] [INFO ]  Ligand STI not found in 3zs5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,187 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,188 [MainThread  ] [INFO ]  ------------ Iteration #188 --------------\n",
      "2021-05-17 15:18:44,188 [MainThread  ] [INFO ]  Cluster member: 3zsg\n",
      "2021-05-17 15:18:44,234 [MainThread  ] [INFO ]  Ligand STI not found in 3zsg cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,235 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,235 [MainThread  ] [INFO ]  ------------ Iteration #189 --------------\n",
      "2021-05-17 15:18:44,236 [MainThread  ] [INFO ]  Cluster member: 3zsh\n",
      "2021-05-17 15:18:44,340 [MainThread  ] [INFO ]  Ligand STI not found in 3zsh cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,341 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,341 [MainThread  ] [INFO ]  ------------ Iteration #190 --------------\n",
      "2021-05-17 15:18:44,342 [MainThread  ] [INFO ]  Cluster member: 3zsi\n",
      "2021-05-17 15:18:44,395 [MainThread  ] [INFO ]  Ligand STI not found in 3zsi cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,396 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,397 [MainThread  ] [INFO ]  ------------ Iteration #191 --------------\n",
      "2021-05-17 15:18:44,397 [MainThread  ] [INFO ]  Cluster member: 3zya\n",
      "2021-05-17 15:18:44,456 [MainThread  ] [INFO ]  Ligand STI not found in 3zya cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,457 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,458 [MainThread  ] [INFO ]  ------------ Iteration #192 --------------\n",
      "2021-05-17 15:18:44,459 [MainThread  ] [INFO ]  Cluster member: 4a9y\n",
      "2021-05-17 15:18:44,519 [MainThread  ] [INFO ]  Ligand STI not found in 4a9y cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,520 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,520 [MainThread  ] [INFO ]  ------------ Iteration #193 --------------\n",
      "2021-05-17 15:18:44,521 [MainThread  ] [INFO ]  Cluster member: 4aa0\n",
      "2021-05-17 15:18:44,624 [MainThread  ] [INFO ]  Ligand STI not found in 4aa0 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,624 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,625 [MainThread  ] [INFO ]  ------------ Iteration #194 --------------\n",
      "2021-05-17 15:18:44,626 [MainThread  ] [INFO ]  Cluster member: 4aa4\n",
      "2021-05-17 15:18:44,677 [MainThread  ] [INFO ]  Ligand STI not found in 4aa4 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,678 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,679 [MainThread  ] [INFO ]  ------------ Iteration #195 --------------\n",
      "2021-05-17 15:18:44,679 [MainThread  ] [INFO ]  Cluster member: 4aa5\n",
      "2021-05-17 15:18:44,717 [MainThread  ] [INFO ]  Ligand STI not found in 4aa5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,718 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,719 [MainThread  ] [INFO ]  ------------ Iteration #196 --------------\n",
      "2021-05-17 15:18:44,719 [MainThread  ] [INFO ]  Cluster member: 4aac\n",
      "2021-05-17 15:18:44,760 [MainThread  ] [INFO ]  Ligand STI not found in 4aac cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,761 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,761 [MainThread  ] [INFO ]  ------------ Iteration #197 --------------\n",
      "2021-05-17 15:18:44,762 [MainThread  ] [INFO ]  Cluster member: 4dli\n",
      "2021-05-17 15:18:44,804 [MainThread  ] [INFO ]  Ligand STI not found in 4dli cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,805 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,805 [MainThread  ] [INFO ]  ------------ Iteration #198 --------------\n",
      "2021-05-17 15:18:44,806 [MainThread  ] [INFO ]  Cluster member: 4dlj\n",
      "2021-05-17 15:18:44,906 [MainThread  ] [INFO ]  Ligand STI not found in 4dlj cluster member, skipping this cluster\n",
      "2021-05-17 15:18:44,907 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:44,908 [MainThread  ] [INFO ]  ------------ Iteration #199 --------------\n",
      "2021-05-17 15:18:44,908 [MainThread  ] [INFO ]  Cluster member: 4e5a\n",
      "2021-05-17 15:18:44,954 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 4e5a\n",
      "2021-05-17 15:18:44,955 [MainThread  ] [INFO ]   \n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:44,956 [MainThread  ] [INFO ]  ------------ Iteration #200 --------------\n",
      "2021-05-17 15:18:44,956 [MainThread  ] [INFO ]  Cluster member: 4e5b\n",
      "2021-05-17 15:18:44,999 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 4e5b\n",
      "2021-05-17 15:18:45,000 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,001 [MainThread  ] [INFO ]  ------------ Iteration #201 --------------\n",
      "2021-05-17 15:18:45,004 [MainThread  ] [INFO ]  Cluster member: 4e6a\n",
      "2021-05-17 15:18:45,056 [MainThread  ] [INFO ]  Ligand STI not found in 4e6a cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,057 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,058 [MainThread  ] [INFO ]  ------------ Iteration #202 --------------\n",
      "2021-05-17 15:18:45,058 [MainThread  ] [INFO ]  Cluster member: 4e6c\n",
      "2021-05-17 15:18:45,097 [MainThread  ] [INFO ]  Ligand STI not found in 4e6c cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,098 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,098 [MainThread  ] [INFO ]  ------------ Iteration #203 --------------\n",
      "2021-05-17 15:18:45,099 [MainThread  ] [INFO ]  Cluster member: 4e8a\n",
      "2021-05-17 15:18:45,201 [MainThread  ] [INFO ]  Ligand STI not found in 4e8a cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,203 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,203 [MainThread  ] [INFO ]  ------------ Iteration #204 --------------\n",
      "2021-05-17 15:18:45,204 [MainThread  ] [INFO ]  Cluster member: 4eh2\n",
      "2021-05-17 15:18:45,243 [MainThread  ] [INFO ]  Ligand STI not found in 4eh2 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,244 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,245 [MainThread  ] [INFO ]  ------------ Iteration #205 --------------\n",
      "2021-05-17 15:18:45,245 [MainThread  ] [INFO ]  Cluster member: 4eh3\n",
      "2021-05-17 15:18:45,284 [MainThread  ] [INFO ]  Ligand STI not found in 4eh3 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,284 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,285 [MainThread  ] [INFO ]  ------------ Iteration #206 --------------\n",
      "2021-05-17 15:18:45,286 [MainThread  ] [INFO ]  Cluster member: 4eh4\n",
      "2021-05-17 15:18:45,326 [MainThread  ] [INFO ]  Ligand STI not found in 4eh4 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,327 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,328 [MainThread  ] [INFO ]  ------------ Iteration #207 --------------\n",
      "2021-05-17 15:18:45,329 [MainThread  ] [INFO ]  Cluster member: 4eh5\n",
      "2021-05-17 15:18:45,422 [MainThread  ] [INFO ]  Ligand STI not found in 4eh5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,423 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,424 [MainThread  ] [INFO ]  ------------ Iteration #208 --------------\n",
      "2021-05-17 15:18:45,424 [MainThread  ] [INFO ]  Cluster member: 4eh6\n",
      "2021-05-17 15:18:45,470 [MainThread  ] [INFO ]  Ligand STI not found in 4eh6 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,471 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,472 [MainThread  ] [INFO ]  ------------ Iteration #209 --------------\n",
      "2021-05-17 15:18:45,473 [MainThread  ] [INFO ]  Cluster member: 4eh7\n",
      "2021-05-17 15:18:45,513 [MainThread  ] [INFO ]  Ligand STI not found in 4eh7 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,513 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,514 [MainThread  ] [INFO ]  ------------ Iteration #210 --------------\n",
      "2021-05-17 15:18:45,515 [MainThread  ] [INFO ]  Cluster member: 4eh8\n",
      "2021-05-17 15:18:45,554 [MainThread  ] [INFO ]  Ligand STI not found in 4eh8 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,555 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,556 [MainThread  ] [INFO ]  ------------ Iteration #211 --------------\n",
      "2021-05-17 15:18:45,556 [MainThread  ] [INFO ]  Cluster member: 4eh9\n",
      "2021-05-17 15:18:45,599 [MainThread  ] [INFO ]  Ligand STI not found in 4eh9 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,599 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,600 [MainThread  ] [INFO ]  ------------ Iteration #212 --------------\n",
      "2021-05-17 15:18:45,601 [MainThread  ] [INFO ]  Cluster member: 4ehv\n",
      "2021-05-17 15:18:45,713 [MainThread  ] [INFO ]  Ligand STI not found in 4ehv cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,714 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,715 [MainThread  ] [INFO ]  ------------ Iteration #213 --------------\n",
      "2021-05-17 15:18:45,716 [MainThread  ] [INFO ]  Cluster member: 4ewq\n",
      "2021-05-17 15:18:45,771 [MainThread  ] [INFO ]  Ligand STI not found in 4ewq cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,772 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,772 [MainThread  ] [INFO ]  ------------ Iteration #214 --------------\n",
      "2021-05-17 15:18:45,773 [MainThread  ] [INFO ]  Cluster member: 4f9w\n",
      "2021-05-17 15:18:45,817 [MainThread  ] [INFO ]  Ligand STI not found in 4f9w cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,818 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,818 [MainThread  ] [INFO ]  ------------ Iteration #215 --------------\n",
      "2021-05-17 15:18:45,819 [MainThread  ] [INFO ]  Cluster member: 4f9y\n",
      "2021-05-17 15:18:45,877 [MainThread  ] [INFO ]  Ligand STI not found in 4f9y cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,878 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,878 [MainThread  ] [INFO ]  ------------ Iteration #216 --------------\n",
      "2021-05-17 15:18:45,879 [MainThread  ] [INFO ]  Cluster member: 4fa2\n",
      "2021-05-17 15:18:45,989 [MainThread  ] [INFO ]  Ligand STI not found in 4fa2 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:45,989 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:45,990 [MainThread  ] [INFO ]  ------------ Iteration #217 --------------\n",
      "2021-05-17 15:18:45,991 [MainThread  ] [INFO ]  Cluster member: 4geo\n",
      "2021-05-17 15:18:46,037 [MainThread  ] [INFO ]  Ligand STI not found in 4geo cluster member, skipping this cluster\n",
      "2021-05-17 15:18:46,038 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:46,038 [MainThread  ] [INFO ]  ------------ Iteration #218 --------------\n",
      "2021-05-17 15:18:46,039 [MainThread  ] [INFO ]  Cluster member: 4ka3\n",
      "2021-05-17 15:18:46,082 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 4ka3\n",
      "2021-05-17 15:18:46,083 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:46,083 [MainThread  ] [INFO ]  ------------ Iteration #219 --------------\n",
      "2021-05-17 15:18:46,084 [MainThread  ] [INFO ]  Cluster member: 4kin\n",
      "2021-05-17 15:18:46,299 [MainThread  ] [INFO ]  Ligand STI not found in 4kin cluster member, skipping this cluster\n",
      "2021-05-17 15:18:46,300 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:46,300 [MainThread  ] [INFO ]  ------------ Iteration #220 --------------\n",
      "2021-05-17 15:18:46,300 [MainThread  ] [INFO ]  Cluster member: 4kip\n",
      "2021-05-17 15:18:46,379 [MainThread  ] [INFO ]  Ligand STI not found in 4kip cluster member, skipping this cluster\n",
      "2021-05-17 15:18:46,379 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:46,380 [MainThread  ] [INFO ]  ------------ Iteration #221 --------------\n",
      "2021-05-17 15:18:46,381 [MainThread  ] [INFO ]  Cluster member: 4kiq\n",
      "2021-05-17 15:18:46,589 [MainThread  ] [INFO ]  Ligand STI not found in 4kiq cluster member, skipping this cluster\n",
      "2021-05-17 15:18:46,589 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:46,591 [MainThread  ] [INFO ]  ------------ Iteration #222 --------------\n",
      "2021-05-17 15:18:46,591 [MainThread  ] [INFO ]  Cluster member: 4l8m\n",
      "2021-05-17 15:18:46,629 [MainThread  ] [INFO ]  Ligand STI not found in 4l8m cluster member, skipping this cluster\n",
      "2021-05-17 15:18:46,630 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:46,631 [MainThread  ] [INFO ]  ------------ Iteration #223 --------------\n",
      "2021-05-17 15:18:46,631 [MainThread  ] [INFO ]  Cluster member: 4loo\n",
      "2021-05-17 15:18:46,746 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 4loo\n",
      "2021-05-17 15:18:46,747 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:46,748 [MainThread  ] [INFO ]  ------------ Iteration #224 --------------\n",
      "2021-05-17 15:18:46,748 [MainThread  ] [INFO ]  Cluster member: 4lop\n",
      "2021-05-17 15:18:46,959 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 4lop\n",
      "2021-05-17 15:18:46,960 [MainThread  ] [INFO ]   \n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:46,961 [MainThread  ] [INFO ]  ------------ Iteration #225 --------------\n",
      "2021-05-17 15:18:46,961 [MainThread  ] [INFO ]  Cluster member: 4loq\n",
      "2021-05-17 15:18:47,185 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 4loq\n",
      "2021-05-17 15:18:47,186 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,187 [MainThread  ] [INFO ]  ------------ Iteration #226 --------------\n",
      "2021-05-17 15:18:47,188 [MainThread  ] [INFO ]  Cluster member: 4r3c\n",
      "2021-05-17 15:18:47,233 [MainThread  ] [INFO ]  Ligand STI not found in 4r3c cluster member, skipping this cluster\n",
      "2021-05-17 15:18:47,234 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,235 [MainThread  ] [INFO ]  ------------ Iteration #227 --------------\n",
      "2021-05-17 15:18:47,235 [MainThread  ] [INFO ]  Cluster member: 4tyh\n",
      "2021-05-17 15:18:47,316 [MainThread  ] [INFO ]  Ligand STI not found in 4tyh cluster member, skipping this cluster\n",
      "2021-05-17 15:18:47,317 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,318 [MainThread  ] [INFO ]  ------------ Iteration #228 --------------\n",
      "2021-05-17 15:18:47,319 [MainThread  ] [INFO ]  Cluster member: 4zth\n",
      "2021-05-17 15:18:47,382 [MainThread  ] [INFO ]  Ligand STI not found in 4zth cluster member, skipping this cluster\n",
      "2021-05-17 15:18:47,383 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,383 [MainThread  ] [INFO ]  ------------ Iteration #229 --------------\n",
      "2021-05-17 15:18:47,384 [MainThread  ] [INFO ]  Cluster member: 5eta\n",
      "2021-05-17 15:18:47,587 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 5eta\n",
      "2021-05-17 15:18:47,588 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,589 [MainThread  ] [INFO ]  ------------ Iteration #230 --------------\n",
      "2021-05-17 15:18:47,590 [MainThread  ] [INFO ]  Cluster member: 5etc\n",
      "2021-05-17 15:18:47,634 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 5etc\n",
      "2021-05-17 15:18:47,634 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,635 [MainThread  ] [INFO ]  ------------ Iteration #231 --------------\n",
      "2021-05-17 15:18:47,636 [MainThread  ] [INFO ]  Cluster member: 5etf\n",
      "2021-05-17 15:18:47,690 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 5etf\n",
      "2021-05-17 15:18:47,691 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,692 [MainThread  ] [INFO ]  ------------ Iteration #232 --------------\n",
      "2021-05-17 15:18:47,693 [MainThread  ] [INFO ]  Cluster member: 5eti\n",
      "2021-05-17 15:18:47,791 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 5eti\n",
      "2021-05-17 15:18:47,792 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,793 [MainThread  ] [INFO ]  ------------ Iteration #233 --------------\n",
      "2021-05-17 15:18:47,793 [MainThread  ] [INFO ]  Cluster member: 5lar\n",
      "2021-05-17 15:18:47,847 [MainThread  ] [INFO ]  Ligand STI not found in 5lar cluster member, skipping this cluster\n",
      "2021-05-17 15:18:47,847 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,848 [MainThread  ] [INFO ]  ------------ Iteration #234 --------------\n",
      "2021-05-17 15:18:47,849 [MainThread  ] [INFO ]  Cluster member: 5ml5\n",
      "2021-05-17 15:18:47,889 [MainThread  ] [INFO ]  Ligand STI not found in 5ml5 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:47,890 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,891 [MainThread  ] [INFO ]  ------------ Iteration #235 --------------\n",
      "2021-05-17 15:18:47,892 [MainThread  ] [INFO ]  Cluster member: 5mtx\n",
      "2021-05-17 15:18:47,933 [MainThread  ] [INFO ]  Ligand STI not found in 5mtx cluster member, skipping this cluster\n",
      "2021-05-17 15:18:47,934 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,935 [MainThread  ] [INFO ]  ------------ Iteration #236 --------------\n",
      "2021-05-17 15:18:47,936 [MainThread  ] [INFO ]  Cluster member: 5mty\n",
      "2021-05-17 15:18:47,986 [MainThread  ] [INFO ]  Ligand STI not found in 5mty cluster member, skipping this cluster\n",
      "2021-05-17 15:18:47,987 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:47,988 [MainThread  ] [INFO ]  ------------ Iteration #237 --------------\n",
      "2021-05-17 15:18:47,989 [MainThread  ] [INFO ]  Cluster member: 5mz3\n",
      "2021-05-17 15:18:48,104 [MainThread  ] [INFO ]  Ligand STI not found in 5mz3 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,105 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,106 [MainThread  ] [INFO ]  ------------ Iteration #238 --------------\n",
      "2021-05-17 15:18:48,107 [MainThread  ] [INFO ]  Cluster member: 5n63\n",
      "2021-05-17 15:18:48,142 [MainThread  ] [INFO ]  Ligand STI not found in 5n63 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,144 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,146 [MainThread  ] [INFO ]  ------------ Iteration #239 --------------\n",
      "2021-05-17 15:18:48,147 [MainThread  ] [INFO ]  Cluster member: 5n64\n",
      "2021-05-17 15:18:48,193 [MainThread  ] [INFO ]  Ligand STI not found in 5n64 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,194 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,194 [MainThread  ] [INFO ]  ------------ Iteration #240 --------------\n",
      "2021-05-17 15:18:48,195 [MainThread  ] [INFO ]  Cluster member: 5n65\n",
      "2021-05-17 15:18:48,241 [MainThread  ] [INFO ]  Ligand STI not found in 5n65 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,242 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,242 [MainThread  ] [INFO ]  ------------ Iteration #241 --------------\n",
      "2021-05-17 15:18:48,243 [MainThread  ] [INFO ]  Cluster member: 5n66\n",
      "2021-05-17 15:18:48,336 [MainThread  ] [INFO ]  Ligand STI not found in 5n66 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,337 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,337 [MainThread  ] [INFO ]  ------------ Iteration #242 --------------\n",
      "2021-05-17 15:18:48,338 [MainThread  ] [INFO ]  Cluster member: 5n67\n",
      "2021-05-17 15:18:48,383 [MainThread  ] [INFO ]  Ligand STI not found in 5n67 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,384 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,385 [MainThread  ] [INFO ]  ------------ Iteration #243 --------------\n",
      "2021-05-17 15:18:48,386 [MainThread  ] [INFO ]  Cluster member: 5n68\n",
      "2021-05-17 15:18:48,435 [MainThread  ] [INFO ]  Ligand STI not found in 5n68 cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,436 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,437 [MainThread  ] [INFO ]  ------------ Iteration #244 --------------\n",
      "2021-05-17 15:18:48,437 [MainThread  ] [INFO ]  Cluster member: 5nzz\n",
      "2021-05-17 15:18:48,803 [MainThread  ] [INFO ]  Ligand STI not found in 5nzz cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,804 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,805 [MainThread  ] [INFO ]  ------------ Iteration #245 --------------\n",
      "2021-05-17 15:18:48,806 [MainThread  ] [INFO ]  Cluster member: 5o8u\n",
      "2021-05-17 15:18:48,855 [MainThread  ] [INFO ]  Ligand STI not found in 5o8u cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,856 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,857 [MainThread  ] [INFO ]  ------------ Iteration #246 --------------\n",
      "2021-05-17 15:18:48,858 [MainThread  ] [INFO ]  Cluster member: 5o8v\n",
      "2021-05-17 15:18:48,901 [MainThread  ] [INFO ]  Ligand STI not found in 5o8v cluster member, skipping this cluster\n",
      "2021-05-17 15:18:48,902 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,903 [MainThread  ] [INFO ]  ------------ Iteration #247 --------------\n",
      "2021-05-17 15:18:48,904 [MainThread  ] [INFO ]  Cluster member: 5o90\n",
      "2021-05-17 15:18:48,954 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 5o90\n",
      "2021-05-17 15:18:48,955 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:48,955 [MainThread  ] [INFO ]  ------------ Iteration #248 --------------\n",
      "2021-05-17 15:18:48,956 [MainThread  ] [INFO ]  Cluster member: 5omg\n",
      "2021-05-17 15:18:49,010 [MainThread  ] [INFO ]  Ligand STI not found in 5omg cluster member, skipping this cluster\n",
      "2021-05-17 15:18:49,011 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,011 [MainThread  ] [INFO ]  ------------ Iteration #249 --------------\n",
      "2021-05-17 15:18:49,012 [MainThread  ] [INFO ]  Cluster member: 5omh\n",
      "2021-05-17 15:18:49,156 [MainThread  ] [INFO ]  Ligand STI not found in 5omh cluster member, skipping this cluster\n",
      "2021-05-17 15:18:49,157 [MainThread  ] [INFO ]   \n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:18:49,158 [MainThread  ] [INFO ]  ------------ Iteration #250 --------------\n",
      "2021-05-17 15:18:49,158 [MainThread  ] [INFO ]  Cluster member: 5tbe\n",
      "2021-05-17 15:18:49,203 [MainThread  ] [INFO ]  Ligand STI not found in 5tbe cluster member, skipping this cluster\n",
      "2021-05-17 15:18:49,204 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,205 [MainThread  ] [INFO ]  ------------ Iteration #251 --------------\n",
      "2021-05-17 15:18:49,205 [MainThread  ] [INFO ]  Cluster member: 5tco\n",
      "2021-05-17 15:18:49,248 [MainThread  ] [INFO ]  Ligand STI not found in 5tco cluster member, skipping this cluster\n",
      "2021-05-17 15:18:49,249 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,249 [MainThread  ] [INFO ]  ------------ Iteration #252 --------------\n",
      "2021-05-17 15:18:49,250 [MainThread  ] [INFO ]  Cluster member: 5uoj\n",
      "2021-05-17 15:18:49,297 [MainThread  ] [INFO ]  No ligands found that could guide the binding site search. Ignoring this member: 5uoj\n",
      "2021-05-17 15:18:49,297 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,298 [MainThread  ] [INFO ]  ------------ Iteration #253 --------------\n",
      "2021-05-17 15:18:49,299 [MainThread  ] [INFO ]  Cluster member: 5wjj\n",
      "2021-05-17 15:18:49,397 [MainThread  ] [INFO ]  Ligand STI not found in 5wjj cluster member, skipping this cluster\n",
      "2021-05-17 15:18:49,398 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,399 [MainThread  ] [INFO ]  ------------ Iteration #254 --------------\n",
      "2021-05-17 15:18:49,400 [MainThread  ] [INFO ]  Cluster member: 5xyx\n",
      "2021-05-17 15:18:49,444 [MainThread  ] [INFO ]  Ligand STI not found in 5xyx cluster member, skipping this cluster\n",
      "2021-05-17 15:18:49,445 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,445 [MainThread  ] [INFO ]  ------------ Iteration #255 --------------\n",
      "2021-05-17 15:18:49,446 [MainThread  ] [INFO ]  Cluster member: 5xyy\n",
      "2021-05-17 15:18:49,488 [MainThread  ] [INFO ]  Ligand STI not found in 5xyy cluster member, skipping this cluster\n",
      "2021-05-17 15:18:49,489 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,490 [MainThread  ] [INFO ]  ------------ Iteration #256 --------------\n",
      "2021-05-17 15:18:49,491 [MainThread  ] [INFO ]  Cluster member: 6anl\n",
      "2021-05-17 15:18:49,536 [MainThread  ] [INFO ]  Ligand STI not found in 6anl cluster member, skipping this cluster\n",
      "2021-05-17 15:18:49,536 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,537 [MainThread  ] [INFO ]  ----------------------------------------\n",
      "2021-05-17 15:18:49,538 [MainThread  ] [INFO ]  All transformed ligand coordinates saved, getting binding site residues\n",
      "2021-05-17 15:18:49,538 [MainThread  ] [INFO ]  Defining binding site residues as those 5.0Å around the 1 cluster superimposed ligands\n",
      "2021-05-17 15:18:49,547 [MainThread  ] [INFO ]  Writing binding site residues into bindingsite.pdb\n",
      "2021-05-17 15:18:49,588 [MainThread  ] [INFO ]   \n",
      "2021-05-17 15:18:49,589 [MainThread  ] [INFO ]  ----------------------------------------\n",
      "2021-05-17 15:18:49,590 [MainThread  ] [INFO ]  Removed temporary folder: 224c5ac9-25fc-4b30-a3b5-de67eeae6bef\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_vs.utils.bindingsite import bindingsite\n",
    "\n",
    "output_bindingsite = \"bindingsite.pdb\"\n",
    "prop = {\n",
    "    \"ligand\": ligand_code,\n",
    "    \"matrix_name\": \"blosum62\",\n",
    "    \"gap_open\": -10.0,\n",
    "    \"gap_extend\": -0.5,\n",
    "    \"max_num_ligands\": 15,\n",
    "    \"radius\": 5\n",
    "}\n",
    "\n",
    "bindingsite(input_pdb_path = pdb_protein,\n",
    "            input_clusters_zip = pdb_cluster,\n",
    "            output_pdb_path = output_bindingsite,\n",
    "            properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"viewPockets\"></a>\n",
    "### Visualizing selected pockets (cavities)\n",
    "Visualizing the selected **pockets** (cavities) from the generated list using **NGL viewer**.<br>\n",
    "\n",
    "**Protein residues** forming the **cavity** are shown in **licorice** representation. **Pockets** are represented in a **greyish surface**. The **original ligand** (if exists) is shown in **green-colored ball and stick** representation. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "88e0fdd9d0ec46fcbe87f161aeed4295",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view = nglview.show_structure_file(download_pdb, default=False)\n",
    "\n",
    "# ligand\n",
    "view[0].add_representation(repr_type='ball+stick', \n",
    "                          selection='STI',\n",
    "                          aspect_ratio=4,\n",
    "                          color='green')\n",
    "\n",
    "view[0].add_representation(repr_type='cartoon', \n",
    "                        selection='not het',\n",
    "                          opacity=.2,\n",
    "                          color='#cccccc')\n",
    "\n",
    "view.add_component(output_bindingsite, default=False)\n",
    "view[1].add_representation(repr_type='surface', \n",
    "                           selection='*', \n",
    "                           opacity = .3,\n",
    "                           radius='1.5',\n",
    "                           lowResolution= True,\n",
    "                           # 0: low resolution \n",
    "                           smooth=1,\n",
    "                           useWorker= True,\n",
    "                           wrap= True)\n",
    "view[1].add_representation(repr_type='licorice', \n",
    "                        selection='*')\n",
    "\n",
    "view[0].center()\n",
    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
    "\n",
    "view.render_image()\n",
    "view.download_image(filename='ngl3.png')\n",
    "view"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src='ngl3.png'></img>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"cavityBox\"></a>\n",
    "***\n",
    "## Generating Cavity Box \n",
    "Generating a **box** surrounding the selected **protein cavity** (pocket), to be used in the **docking procedure**. The **box** is defining the region on the **surface** of the **protein target** where the **docking program** should explore a possible **ligand dock**.<br>\n",
    "An offset of **12 Angstroms** is used to generate a **big enough box** to fit the **small molecule** and its possible rotations.<br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [box](https://biobb-vs.readthedocs.io/en/latest/utils.html#module-utils.box) from **biobb_vs.utils.box**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:19:10,748 [MainThread  ] [INFO ]  Loading residue PDB selection from bindingsite.pdb\n",
      "2021-05-17 15:19:10,750 [MainThread  ] [INFO ]  Binding site center (Angstroms):     16.790    -4.357   -20.224\n",
      "2021-05-17 15:19:10,751 [MainThread  ] [INFO ]  Adding 12.0 Angstroms offset\n",
      "2021-05-17 15:19:10,753 [MainThread  ] [INFO ]  Binding site size (Angstroms):       23.958    25.097    25.515\n",
      "2021-05-17 15:19:10,754 [MainThread  ] [INFO ]  Volume (cubic Angstroms): 122738\n",
      "2021-05-17 15:19:10,755 [MainThread  ] [INFO ]  Adding box coordinates\n",
      "2021-05-17 15:19:10,756 [MainThread  ] [INFO ]  Saving output PDB file (with box setting annotations): box.pdb\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_vs.utils.box import box\n",
    "\n",
    "output_box = \"box.pdb\"\n",
    "prop = {\n",
    "    \"offset\": 12,\n",
    "    \"box_coordinates\": True\n",
    "}\n",
    "\n",
    "box(input_pdb_path = output_bindingsite,\n",
    "            output_pdb_path = output_box,\n",
    "            properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"vis3D\"></a>\n",
    "### Visualizing binding site box in 3D structure\n",
    "Visualizing the **protein structure**, the **selected cavity**, and the **generated box**, all together using **NGL** viewer. Using the **original structure** with the **small ligand** inside (Imatinib, [STI](https://www.rcsb.org/ligand/STI)), to check that the **selected cavity** is placed in the **same region** as the **original ligand**. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d430f3f67f6b405781c87c1d12a4d5f9",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#view = nglview.show_structure_file(box, default=False)\n",
    "view = nglview.NGLWidget()\n",
    "#s = view.add_component(pdb_single_chain)\n",
    "s = view.add_component(download_pdb)\n",
    "b = view.add_component(output_box)\n",
    "s = view.add_component(output_bindingsite)\n",
    "\n",
    "atomPair = [\n",
    "    [ \"9999:Z.ZN1\", \"9999:Z.ZN2\" ],\n",
    "    [ \"9999:Z.ZN2\", \"9999:Z.ZN4\" ],\n",
    "    [ \"9999:Z.ZN4\", \"9999:Z.ZN3\" ],\n",
    "    [ \"9999:Z.ZN3\", \"9999:Z.ZN1\" ],\n",
    "    \n",
    "    [ \"9999:Z.ZN5\", \"9999:Z.ZN6\" ],\n",
    "    [ \"9999:Z.ZN6\", \"9999:Z.ZN8\" ],\n",
    "    [ \"9999:Z.ZN8\", \"9999:Z.ZN7\" ],\n",
    "    [ \"9999:Z.ZN7\", \"9999:Z.ZN5\" ],\n",
    "    \n",
    "    [ \"9999:Z.ZN1\", \"9999:Z.ZN5\" ],\n",
    "    [ \"9999:Z.ZN2\", \"9999:Z.ZN6\" ],\n",
    "    [ \"9999:Z.ZN3\", \"9999:Z.ZN7\" ],\n",
    "    [ \"9999:Z.ZN4\", \"9999:Z.ZN8\" ]\n",
    "]\n",
    "\n",
    "#view.shape.add_cylinder( [ 0, 2, 7 ], [ 10, 0, 9 ], [ 1, 0, 0 ], 0.1 )\n",
    "\n",
    "# structure\n",
    "s.add_representation(repr_type='cartoon', \n",
    "                        selection='not het',\n",
    "                        color='#cccccc',\n",
    "                       opacity=.2)\n",
    "# ligands box\n",
    "b.add_representation(repr_type='ball+stick', \n",
    "                        selection='9999',\n",
    "                        color='pink',\n",
    "                       aspectRatio = 10)\n",
    "# lines box\n",
    "b.add_representation(repr_type='distance', \n",
    "                        atomPair= atomPair,\n",
    "                       labelColor= 'transparent',\n",
    "                       color= 'black')\n",
    "\n",
    "# output bindingsite\n",
    "s.add_representation(repr_type='surface', \n",
    "                        selection='*', \n",
    "                        color='skyblue',\n",
    "                        lowResolution= True,\n",
    "                        # 0: low resolution \n",
    "                        smooth=1,\n",
    "                        surfaceType= 'av', \n",
    "                        contour=True,\n",
    "                        opacity=0.4,\n",
    "                        useWorker= True,\n",
    "                        wrap= True)\n",
    "\n",
    "\n",
    "view.center()\n",
    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
    "\n",
    "view.render_image()\n",
    "view.download_image(filename='ngl4.png')\n",
    "view"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src='ngl4.png'></img>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"downloadSmallMolecule\"></a>\n",
    "***\n",
    "## Downloading Small Molecule \n",
    "Downloading the desired **small molecule** to be used in the **docking procedure**. <br>\n",
    "In this particular example, the small molecule of interest is the FDA-approved drug **Imatinib**, with PDB code **STI**.<br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [ideal_sdf](https://biobb-io.readthedocs.io/en/latest/api.html#module-api.ideal_sdf) from **biobb_io.api.ideal_sdf**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:19:27,272 [MainThread  ] [INFO ]  Downloading: STI from: ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/sdf/STI.sdf\n",
      "2021-05-17 15:19:27,275 [MainThread  ] [INFO ]  Writting sdf to: ideal.sdf\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_io.api.ideal_sdf import ideal_sdf\n",
    "\n",
    "sdf_ideal = \"ideal.sdf\"\n",
    "prop = {\n",
    "  \"ligand_code\": ligand_code\n",
    "}\n",
    "\n",
    "ideal_sdf(output_sdf_path=sdf_ideal,\n",
    "    properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"sdf2pdb\"></a>\n",
    "***\n",
    "## Converting Small Molecule \n",
    "Converting the desired **small molecule** to be used in the **docking procedure**, from **SDF** format to **PDB** format using the **OpenBabel chemoinformatics** tool. <br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [babel_convert](https://biobb-chemistry.readthedocs.io/en/latest/babelm.html#module-babelm.babel_convert) from **biobb_chemistry.babelm.babel_convert**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:19:29,300 [MainThread  ] [INFO ]  Value  is not compatible as a coordinates value\n",
      "2021-05-17 15:19:29,302 [MainThread  ] [INFO ]  Not using any container\n",
      "2021-05-17 15:19:29,419 [MainThread  ] [INFO ]  obabel -isdf ideal.sdf -opdb -Oligand.pdb  \n",
      "\n",
      "2021-05-17 15:19:29,420 [MainThread  ] [INFO ]  Exit code 0\n",
      "\n",
      "2021-05-17 15:19:29,421 [MainThread  ] [INFO ]  1 molecule converted\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_chemistry.babelm.babel_convert import babel_convert\n",
    "\n",
    "ligand = \"ligand.pdb\"\n",
    "prop = {\n",
    "    \"input_format\": \"sdf\",\n",
    "    \"output_format\": \"pdb\",\n",
    "    \"obabel_path\": \"obabel\"\n",
    "}\n",
    "\n",
    "babel_convert(input_path = sdf_ideal,\n",
    "            output_path = ligand,\n",
    "            properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"ligand_pdb2pdbqt\"></a>\n",
    "***\n",
    "## Preparing Small Molecule (ligand) for Docking\n",
    "Preparing the **small molecule** structure for the **docking procedure**. Converting the **PDB file** to a **PDBQT file** format (AutoDock PDBQT: Protein Data Bank, with Partial Charges (Q), & Atom Types (T)), needed by **AutoDock Vina**. <br><br>\n",
    "The process adds **partial charges** and **atom types** to every atom. Besides, the **ligand flexibility** is also defined in the information contained in the file. The concept of **\"torsion tree\"** is used to represent the **rigid and rotatable** pieces of the **ligand**. A rigid piece (**\"root\"**) is defined, with zero or more rotatable pieces (**\"branches\"**), hanging from the root, and defining the **rotatable bonds**.<br><br>\n",
    "More info about **PDBQT file format** can be found in the [AutoDock FAQ pages](http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file).\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [babel_convert](https://biobb-chemistry.readthedocs.io/en/latest/babelm.html#module-babelm.babel_convert) from **biobb_chemistry.babelm.babel_convert**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:19:31,878 [MainThread  ] [INFO ]  Value  is not compatible as a coordinates value\n",
      "2021-05-17 15:19:31,879 [MainThread  ] [INFO ]  Not using any container\n",
      "2021-05-17 15:19:31,951 [MainThread  ] [INFO ]  obabel -ipdb ligand.pdb -opdbqt -Oprep_ligand.pdbqt  \n",
      "\n",
      "2021-05-17 15:19:31,953 [MainThread  ] [INFO ]  Exit code 0\n",
      "\n",
      "2021-05-17 15:19:31,953 [MainThread  ] [INFO ]  1 molecule converted\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_chemistry.babelm.babel_convert import babel_convert\n",
    "\n",
    "prep_ligand = \"prep_ligand.pdbqt\"\n",
    "prop = {\n",
    "    \"input_format\": \"pdb\",\n",
    "    \"output_format\": \"pdbqt\",\n",
    "    \"obabel_path\": \"obabel\"\n",
    "}\n",
    "\n",
    "babel_convert(input_path = ligand,\n",
    "            output_path = prep_ligand,\n",
    "            properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"viewDrug\"></a>\n",
    "### Visualizing small molecule (drug)\n",
    "Visualizing the desired **drug** to be docked to the **target protein**, using **NGL viewer**.<br>\n",
    "- **Left panel**: **PDB-formatted** file, with all hydrogen atoms.\n",
    "- **Right panel**: **PDBqt-formatted** file (AutoDock Vina-compatible), with **united atom model** (only polar hydrogens are placed in the structures to correctly type heavy atoms as hydrogen bond donors).\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "a4e8831a0a654df69a28cdc8494712f6",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HBox(children=(NGLWidget(), NGLWidget()))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from ipywidgets import HBox\n",
    "\n",
    "v0 = nglview.show_structure_file(ligand)\n",
    "v1 = nglview.show_structure_file(prep_ligand)\n",
    "\n",
    "v0._set_size('500px', '')\n",
    "v1._set_size('500px', '')\n",
    "\n",
    "def on_change(change):\n",
    "    v1._set_camera_orientation(change['new'])\n",
    "    \n",
    "v0.observe(on_change, ['_camera_orientation'])\n",
    "\n",
    "HBox([v0, v1])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src='ngl5.png'></img>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"protein_pdb2pdbqt\"></a>\n",
    "***\n",
    "## Preparing Target Protein for Docking\n",
    "Preparing the **target protein** structure for the **docking procedure**. Converting the **PDB file** to a **PDBqt file**, needed by **AutoDock Vina**. Similarly to the previous step, the process adds **partial charges** and **atom types** to every target protein atom. In this case, however, we are not taking into account **receptor flexibility**, although **Autodock Vina** allows some limited flexibility of selected **receptor side chains** [(see the documentation)](https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html).<br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [str_check_add_hydrogens](https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#utils-str-check-add-hydrogens-module) from **biobb_structure_utils.utils.str_check_add_hydrogens**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:19:44,142 [MainThread  ] [INFO ]  check_structure -i /home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/pdb_protein.pdb -o prep_receptor.pdbqt --force_save add_hydrogen --add_charges --add_mode auto\n",
      "\n",
      "2021-05-17 15:19:44,143 [MainThread  ] [INFO ]  Exit code 0\n",
      "\n",
      "2021-05-17 15:19:44,144 [MainThread  ] [INFO ]  ===============================================================================\n",
      "=                   BioBB structure checking utility v3.7.2                   =\n",
      "=                 A. Hospital, P. Andrio, J.L. Gelpi 2018-20                  =\n",
      "===============================================================================\n",
      "\n",
      "Warning: sequence features only available in mmCIF format or with external fasta input\n",
      "Structure /home/gbayarri_local/projects/BioBB/tutorials/biobb_wf_virtual-screening/biobb_wf_virtual-screening/notebooks/clusterBindingSite/pdb_protein.pdb loaded\n",
      " Title: \n",
      " Experimental method: unknown\n",
      " Resolution: None A\n",
      "\n",
      " Num. models: 1\n",
      " Num. chains: 1 (A: Protein)\n",
      " Num. residues:  329\n",
      " Num. residues with ins. codes:  0\n",
      " Num. HETATM residues:  0\n",
      " Num. ligands or modified residues:  0\n",
      " Num. water mol.:  0\n",
      " Num. atoms:  2668\n",
      "\n",
      "Running add_hydrogen. Options: --add_charges --add_mode auto\n",
      "107 Residues requiring selection on adding H atoms\n",
      "CYS A39,A119,A162,A211\n",
      "ASP A43,A88,A101,A112,A124,A125,A145,A150,A161,A168,A205,A227,A230,A283,A292,A294,A313,A315,A316,A321,A324,A331,A335,A343\n",
      "GLU A12,A19,A22,A71,A81,A97,A98,A160,A163,A192,A215,A245,A253,A286,A317,A328,A336,A344\n",
      "HIS A64,A77,A80,A107,A126,A142,A148,A199,A228,A305,A312\n",
      "LYS A15,A45,A53,A54,A66,A76,A79,A118,A121,A139,A152,A165,A233,A248,A249,A267,A287,A295,A338\n",
      "ARG A5,A10,A23,A49,A57,A67,A70,A73,A94,A136,A149,A186,A189,A220,A237,A256,A296,A330\n",
      "TYR A9,A24,A69,A103,A132,A140,A188,A200,A258,A307,A311,A323,A342\n",
      "WARNING: fixing side chains, override with --no_fix_side\n",
      "Running fixside. Options: --fix all\n",
      "1 Residues with missing side chain atoms found\n",
      " PRO A352   \n",
      "Fixing side chains\n",
      "PRO A352\n",
      "Fixed 1 side chain(s)\n",
      "Checking for steric clashes\n",
      "No severe clashes detected\n",
      "No apolar clashes detected\n",
      "No polar_acceptor clashes detected\n",
      "No polar_donor clashes detected\n",
      "No positive clashes detected\n",
      "No negative clashes detected\n",
      "Selection: auto\n",
      "Replacing HIS A64 by HIE\n",
      "Replacing HIS A77 by HIE\n",
      "Replacing HIS A80 by HIE\n",
      "Replacing HIS A107 by HIE\n",
      "Replacing HIS A126 by HIE\n",
      "Replacing HIS A142 by HIE\n",
      "Replacing HIS A148 by HIE\n",
      "Replacing HIS A199 by HIE\n",
      "Replacing HIS A228 by HIE\n",
      "Replacing HIS A305 by HIE\n",
      "Replacing HIS A312 by HIE\n",
      "Updating partial charges and atom types\n",
      "Warning: OXT atom missing in CGLY A31. Run backbone --add_atoms first\n",
      "Warning: OXT atom missing in CPHE A169. Run backbone --add_atoms first\n",
      "Warning: OXT atom missing in CPRO A352. Run backbone --add_atoms first\n",
      "Total assigned charge:      -2.07\n",
      "Final Num. models: 1\n",
      "Final Num. chains: 1 (A: Protein)\n",
      "Final Num. residues:  329\n",
      "Final Num. residues with ins. codes:  0\n",
      "Final Num. HETATM residues:  0\n",
      "Final Num. ligands or modified residues:  0\n",
      "Final Num. water mol.:  0\n",
      "Final Num. atoms:  5353\n",
      "Structure saved on prep_receptor.pdbqt\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_structure_utils.utils.str_check_add_hydrogens import str_check_add_hydrogens\n",
    "\n",
    "prep_receptor = \"prep_receptor.pdbqt\"\n",
    "prop = {\n",
    "    \"charges\": True,\n",
    "    \"mode\": \"auto\"\n",
    "}\n",
    "\n",
    "str_check_add_hydrogens(input_structure_path = pdb_protein,\n",
    "            output_structure_path = prep_receptor,\n",
    "            properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"docking\"></a>\n",
    "***\n",
    "## Running the Docking\n",
    "Running the **docking process** with the prepared files:\n",
    "- **ligand**\n",
    "- **target protein**\n",
    "- **binding site box**<br>\n",
    "\n",
    "using **AutoDock Vina**. <br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [autodock_vina_run](https://biobb-vs.readthedocs.io/en/latest/vina.html#module-vina.autodock_vina_run) from **biobb_vs.vina.autodock_vina_run**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:19:47,166 [MainThread  ] [INFO ]  prep_receptor.pdbqt file ends with END, cleaning\n",
      "2021-05-17 15:19:47,171 [MainThread  ] [INFO ]  Executing AutoDock Vina\n",
      "2021-05-17 15:19:47,172 [MainThread  ] [INFO ]  Not using any container\n",
      "2021-05-17 15:20:27,135 [MainThread  ] [INFO ]  vina --ligand prep_ligand.pdbqt --receptor prep_receptor.pdbqt --center_x=16.790 --center_y=-4.357 --center_z=-20.224 --size_x=23.958 --size_y=25.097 --size_z=25.515 --out output_vina.pdbqt --log output_vina.log\n",
      "\n",
      "2021-05-17 15:20:27,136 [MainThread  ] [INFO ]  Exit code 0\n",
      "\n",
      "2021-05-17 15:20:27,137 [MainThread  ] [INFO ]  #################################################################\n",
      "# If you used AutoDock Vina in your work, please cite:          #\n",
      "#                                                               #\n",
      "# O. Trott, A. J. Olson,                                        #\n",
      "# AutoDock Vina: improving the speed and accuracy of docking    #\n",
      "# with a new scoring function, efficient optimization and       #\n",
      "# multithreading, Journal of Computational Chemistry 31 (2010)  #\n",
      "# 455-461                                                       #\n",
      "#                                                               #\n",
      "# DOI 10.1002/jcc.21334                                         #\n",
      "#                                                               #\n",
      "# Please see http://vina.scripps.edu for more information.      #\n",
      "#################################################################\n",
      "\n",
      "Detected 8 CPUs\n",
      "Reading input ... done.\n",
      "Setting up the scoring function ... done.\n",
      "Analyzing the binding site ... done.\n",
      "Using random seed: -2066523565\n",
      "Performing search ... \n",
      "0%   10   20   30   40   50   60   70   80   90   100%\n",
      "|----|----|----|----|----|----|----|----|----|----|\n",
      "***************************************************\n",
      "done.\n",
      "Refining results ... done.\n",
      "\n",
      "mode |   affinity | dist from best mode\n",
      "     | (kcal/mol) | rmsd l.b.| rmsd u.b.\n",
      "-----+------------+----------+----------\n",
      "   1        -11.1      0.000      0.000\n",
      "   2         -9.5      8.143     14.750\n",
      "   3         -9.4      2.244     12.610\n",
      "   4         -9.1      2.555     12.320\n",
      "   5         -9.0      7.623     12.348\n",
      "   6         -9.0      6.489     13.143\n",
      "   7         -8.9      2.323     11.749\n",
      "   8         -8.6      5.768     13.052\n",
      "   9         -8.4      7.102     12.358\n",
      "Writing output ... done.\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_vs.vina.autodock_vina_run import autodock_vina_run\n",
    "\n",
    "output_vina_pdbqt = \"output_vina.pdbqt\"\n",
    "output_vina_log = \"output_vina.log\"\n",
    "\n",
    "autodock_vina_run(input_ligand_pdbqt_path = prep_ligand,\n",
    "             input_receptor_pdbqt_path = prep_receptor,\n",
    "             input_box_path = output_box,\n",
    "            output_pdbqt_path = output_vina_pdbqt,\n",
    "             output_log_path = output_vina_log)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"viewDocking\"></a>\n",
    "### Visualizing docking output poses\n",
    "Visualizing the generated **docking poses** for the **ligand**, using **NGL viewer**. <br>\n",
    "- **Left panel**: **Docking poses** displayed with atoms coloured by **partial charges** and **licorice** representation.\n",
    "- **Right panel**: **Docking poses** displayed with atoms coloured by **element** and **ball-and-stick** representation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "265bed946dec4d639059716734f746c6",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HBox(children=(NGLWidget(), NGLWidget()))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "models = 'all'\n",
    "#models = '/0 or /1 or /4'\n",
    "\n",
    "v0 = nglview.show_structure_file(output_vina_pdbqt, default=False)\n",
    "v0.add_representation(repr_type='licorice', \n",
    "                        selection=models,\n",
    "                       colorScheme= 'partialCharge')\n",
    "v0.center()\n",
    "v1 = nglview.show_structure_file(output_vina_pdbqt, default=False)\n",
    "v1.add_representation(repr_type='ball+stick', \n",
    "                        selection=models)\n",
    "v1.center()\n",
    "\n",
    "v0._set_size('500px', '')\n",
    "v1._set_size('500px', '')\n",
    "\n",
    "def on_change(change):\n",
    "    v1._set_camera_orientation(change['new'])\n",
    "    \n",
    "v0.observe(on_change, ['_camera_orientation'])\n",
    "\n",
    "HBox([v0, v1])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src='ngl6.png'></img>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"selectPose\"></a>\n",
    "### Select Docking Pose\n",
    "Select a specific **docking pose** from the output list for **visual inspection**.\n",
    "<br>\n",
    "Choose a **docking pose** from the **DropDown list**."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "efb4a08e461a4170a2590434f77a824f",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Dropdown(description='Sel. model:', options=(('model0', 0), ('model1', 1), ('model2', 2), ('model3', 3), ('mod…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from Bio.PDB import PDBParser\n",
    "parser = PDBParser(QUIET = True)\n",
    "structure = parser.get_structure(\"protein\", output_vina_pdbqt)\n",
    "models = []\n",
    "for i, m in enumerate(structure):\n",
    "    models.append(('model' + str(i), i))\n",
    "    \n",
    "mdsel = ipywidgets.Dropdown(\n",
    "    options=models,\n",
    "    description='Sel. model:',\n",
    "    disabled=False,\n",
    ")\n",
    "display(mdsel)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"extractPose\"></a>\n",
    "***\n",
    "## Extract a Docking Pose\n",
    "Extract a specific **docking pose** from the **docking** outputs. <br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [extract_model_pdbqt](https://biobb-vs.readthedocs.io/en/latest/utils.html#module-utils.extract_model_pdbqt) from **biobb_vs.utils.extract_model_pdbqt**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:20:41,685 [MainThread  ] [INFO ]  Saving model 1 to output_model.pdbqt\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_vs.utils.extract_model_pdbqt import extract_model_pdbqt\n",
    "\n",
    "output_pdbqt_model = \"output_model.pdbqt\"\n",
    "prop = {\n",
    "    \"model\": 1\n",
    "}\n",
    "\n",
    "extract_model_pdbqt(input_pdbqt_path = output_vina_pdbqt,\n",
    "             output_pdbqt_path = output_pdbqt_model,\n",
    "            properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"pdbqt2pdb\"></a>\n",
    "***\n",
    "## Converting Ligand Pose to PDB format\n",
    "Converting **ligand pose** to **PDB format**. <br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [babel_convert](https://biobb-chemistry.readthedocs.io/en/latest/babelm.html#module-babelm.babel_convert) from **biobb_chemistry.babelm.babel_convert**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:20:44,121 [MainThread  ] [INFO ]  Value  is not compatible as a coordinates value\n",
      "2021-05-17 15:20:44,123 [MainThread  ] [INFO ]  Not using any container\n",
      "2021-05-17 15:20:44,172 [MainThread  ] [INFO ]  obabel -ipdbqt output_model.pdbqt -opdb -Ooutput_model.pdb  \n",
      "\n",
      "2021-05-17 15:20:44,176 [MainThread  ] [INFO ]  Exit code 0\n",
      "\n",
      "2021-05-17 15:20:44,178 [MainThread  ] [INFO ]  1 molecule converted\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_chemistry.babelm.babel_convert import babel_convert\n",
    "\n",
    "output_pdb_model = \"output_model.pdb\"\n",
    "prop = {\n",
    "    \"input_format\": \"pdbqt\",\n",
    "    \"output_format\": \"pdb\",\n",
    "    \"obabel_path\": \"obabel\"\n",
    "}\n",
    "\n",
    "babel_convert(input_path = output_pdbqt_model,\n",
    "             output_path = output_pdb_model,\n",
    "            properties=prop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"catPdb\"></a>\n",
    "***\n",
    "## Superposing Ligand Pose to the Target Protein Structure\n",
    "Superposing **ligand pose** to the target **protein structure**, in order to see the **protein-ligand docking conformation**. <br><br>Building a new **PDB file** with both **target and ligand** (binding pose) structures. <br>\n",
    "\n",
    "***\n",
    "**Building Blocks** used:\n",
    " - [cat_pdb](https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.cat_pdb) from **biobb_structure_utils.utils.cat_pdb**\n",
    "***"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2021-05-17 15:20:46,424 [MainThread  ] [INFO ]  File output_structure.pdb created\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from biobb_structure_utils.utils.cat_pdb import cat_pdb\n",
    "\n",
    "output_structure = \"output_structure.pdb\"\n",
    "\n",
    "cat_pdb(input_structure1 = pdb_protein,\n",
    "             input_structure2 = output_pdb_model,\n",
    "             output_structure_path = output_structure)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a id=\"viewFinal\"></a>\n",
    "### Comparing final result with experimental structure \n",
    "Visualizing and comparing the generated **protein-ligand** complex with the original **protein-ligand conformation** (downloaded from the PDB database), using **NGL viewer**. <br>\n",
    "- **Licorice, element-colored** representation: **Experimental pose**.\n",
    "- **Licorice, green-colored** representation: **Docking pose**.\n",
    "<br>\n",
    "\n",
    "Note that outputs from **AutoDock Vina** don't contain all the atoms, as the program works with a **united-atom representation** (i.e. only polar hydrogens)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d58919dff1094b85a7e894ee741063bf",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view = nglview.NGLWidget()\n",
    "\n",
    "# v1 = Experimental Structure\n",
    "v1 = view.add_component(download_pdb)\n",
    "\n",
    "v1.clear()\n",
    "v1.add_representation(repr_type='licorice', \n",
    "                     selection='STI',\n",
    "                     radius=0.5)\n",
    "\n",
    "# v2 = Docking result\n",
    "v2 = view.add_component(output_structure)\n",
    "v2.clear()\n",
    "v2.add_representation(repr_type='cartoon', colorScheme = 'sstruc')\n",
    "v2.add_representation(repr_type='licorice', radius=0.5, color= 'green', selection='UNL')\n",
    "\n",
    "view._remote_call('setSize', target='Widget', args=['','600px'])\n",
    "view\n",
    "\n",
    "# align reference and output\n",
    "code = \"\"\"\n",
    "var stage = this.stage;\n",
    "var clist_len = stage.compList.length;\n",
    "var i = 0;\n",
    "var s = [];\n",
    "for(i = 0; i <= clist_len; i++){\n",
    "    if(stage.compList[i] != undefined && stage.compList[i].structure != undefined) {        \n",
    "       s.push(stage.compList[i])\n",
    "    }\n",
    "}\n",
    "NGL.superpose(s[0].structure, s[1].structure, true, \".CA\")\n",
    "s[ 0 ].updateRepresentations({ position: true })\n",
    "s[ 0 ].autoView()\n",
    "\"\"\"\n",
    "\n",
    "view._execute_js_code(code)\n",
    "\n",
    "view.render_image()\n",
    "view.download_image(filename='ngl7.png')\n",
    "view"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src='ngl7.png'></img>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "***\n",
    "<a id=\"questions\"></a>\n",
    "\n",
    "## Questions & Comments\n",
    "\n",
    "Questions, issues, suggestions and comments are really welcome!\n",
    "\n",
    "* GitHub issues:\n",
    "    * [https://github.com/bioexcel/biobb](https://github.com/bioexcel/biobb)\n",
    "\n",
    "* BioExcel forum:\n",
    "    * [https://ask.bioexcel.eu/c/BioExcel-Building-Blocks-library](https://ask.bioexcel.eu/c/BioExcel-Building-Blocks-library)\n"
   ]
  }
 ],
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